In front of a full house at Xconomy’s first public Big Apple event—New York Life Sciences 2031—biotech entrepreneurs Sam Waksal and Eric Schadt wagered on the likelihood that computers would overtake human scientists in the quest to develop drugs. Schadt pointed to IBM’s Watson as an example of a computer performing better than humans at a complex task (namely winning the game show Jeopardy), and he predicted that the drug industry would be altered significantly by bioinformatics, or the use of computation and artificial intelligence to translate genomic information into useable therapies. Replied Waksal: “Sequencing every gene isn’t going to reposition every drug to make it work. Drug discovery is a different science. It can’t be done by some computer.”

Schadt is the chief scientific officer of Pacific Biosciences and the new head of the Mount Sinai Institute for Genomics and Multiscale Biology. Waksal is the founder and former CEO of ImClone Systems and the founder and current CEO of biotech startup Kadmon. They were joined in the lively panel discussion by Barbara Dalton, vice president of venture capital for Pfizer, Samuel Isaly, managing partner of OrbiMed Advisors, and moderator Les Funtleyder, portfolio manager of the Miller Tabak Health Care Transformation Fund.

The after-work panel event took place at the Alexandria Center for Life Sciences on New York’s east side. Our audience of more than 150 participated enthusiastically, lobbing questions at the panelists, and tweeting highlights of the night’s discussion on our Twitter feed, #NY2031. (Search that hashtag on Twitter and you can follow the events as they happened in real time.)

The discussion started with each panelist making his or her prediction for where life sciences would be 20 years from now. Said Funtleyder: “My vision is that we will have our genetic sequences and our electronic medical records on our smartphones. We will go to a doctor that has been directed to us by a crowd-sourced social network and … Next Page »

Comments | Reprints | Share:          

Illumina CEO Jay Flatley memorably called the bioinformatics industry “road kill” in an interview with Xconomy about 18 months ago. But have new opportunities started to emerge for genomic software startups now that scientists are really, Really, Really! crying out for better software to manage the data deluge?

After all, isn’t the genomic data going to become truly overwhelming for scientists to sort through when whole human genomes, at 6 billion DNA data points apiece, can be obtained for a few thousand bucks and a few days of work?

This is one of the fascinating questions we’re going to dive into on October 24 at Xconomy’s next big public event in San Francisco, titled “Computing in the Age of the $1,000 Genome.” It will be part of a half-day forum hosted by QB3, the biotech startup incubator at UCSF’s Mission Bay campus, in Genentech Hall.

We have an awesome lineup of entrepreneurs who will appear smack in the middle of this conference, after we plan to kick things off with a keynote chat with Complete Genomics CEO Cliff Reid and PacBio CEO Hugh Martin. Here’s who you can expect to hear talking about the new opportunities in bioinformatics.

—Rob Arnold, the general manager of the Geospiza division of Waltham, MA-based PerkinElmer (NYSE: PKI). Rob was previously the president of Geospiza, one of the longstanding survivors from the previous genomics/bioinformatics bubble period of the early 2000s. Geospiza made it through some lean years, competing against open source software, and built a big enough customer list to get acquired in May by life sciences tools giant PerkinElmer.

—Andreas Sundquist, the co-founder and CEO of Mountain View, CA-based DNAnexus. Sundquist, who cut his teeth in computational biology during his grad school years at Stanford, has brought a decidedly Web 2.0, easy-to-use style to its offerings that are supposed to make it easier for average biologists to interact with all their genomic data. This year, he’s found a way to make DNAnexus software relevant to two of the Valley’s emerging sequencing players—Complete Genomics and PacBio.

—Doug Bassett, the chief scientific officer of Redwood City, CA-based Ingenuity Systems, will be able to talk about his company has found a niche in crunching not just genomic data, but in connecting the dots with all the other relevant ‘omics data—proteomics, metabolomics, etc, and how it all might be useful for pharmaceutical R&D. Bassett knows what it’s like to try to separate the signal from the noise from the customer’s side of things—he was previously the executive director molecular profiling for Merck’s Rosetta Inpharmatics division.

—And last but not least on this panel is Ilya Kupershmidt, the co-founder and vice president of products for Cupertino, CA-based NextBio. This company has found a way to turn a profit by finding a way to pool genomic data from free public databases like those kept by the NIH, along with the private, proprietary data generated in-house at pharma and biotech companies. NextBio has assembled a prominent group of customers for this service, including Merck, Johnson & Johnson, and Pfizer, as well as academic leaders like The Scripps Research Institute, Stanford University, and the Sanford-Burnham Medical Research Institute.

I expect these guys to have lots of insights into how the market has changed for bioinformatics in just the last six months or so as sequencing has gotten much cheaper, and demand has gotten higher. And this is really just one aspect of the overall event, which will feature other great speakers on the medical and societal implications of all this work to generate genomic data and analyze it. You can get tickets here at the registration page. See you on the 24th.

Comments (5) | Reprints | Share:          

This week’s New England life sciences news spanned companies targeting cancer, schizophrenia, sleep improvement, and genomic analysis.

—Newton, MA-based health IT startup Zeo announced it added a mobile app version of its sleep tracking and coaching system. The company hopes the tool, which pushes sleep data gathered from a sensor-laden headband to a user’s mobile interface, can be integrated with other apps focused on improving wellness.

—RXi Pharmaceuticals (NASDAQ: RXII) of Worcester, MA, announced that it will divide its work on RNA therapeutics from other pursuits, by splitting up into two publicly traded companies. Galena Biopharma, one of the companies, will pursue cancer treatments, while RXi will continue work in RNA interference—molecules that silence disease-causing genes—through developing RXI-109, its drug candidate for treating fibrosis and scarring.

—Boston-based Acetylon Pharmaceuticals, a biotech startup backed by the holding group of New England Patriots owner Robert Kraft, started a human trial of one of its cancer drugs (ACY-1215) that fights the disease by targeting enzymes related to gene expression.

—Karuna Pharmaceuticals, a startup incubated at Boston’s PureTech Ventures and led by ex-Pfizer exec Ed Harrigan, announced it had licensed a group of experimental schizophrenia drugs from Nashville-based Vanderbilt University. The compounds are believed to treat schizophrenia symptoms such as memory loss and the inability to experience pleasure or to carry on normal social interactions, which aren’t currently addressed on the market.

—Cambridge, MA-based Knome is expanding its genomics analysis businesses beyond the mega-wealthy, by targeting researchers in bioinformatics and other fields, my colleague Luke wrote.

Comments | Reprints | Share:          

There seemed to be a spate of financings among San Diego’s life sciences companies in recent weeks, and some local CEOs are telling me more deals are in the works. Your briefing begins now.

—San Diego has added another startup to its growing cluster of companies developing next-generation genome sequencing and molecular diagnosis technologies. BioNanomatrix, which has raised nearly $29 million to develop its proprietary nano-scale DNA mapping technology, said it has moved its headquarters from Philadelphia to San Diego’s Torrey Pines mesa.

—Awarepoint‘s new CEO, Jay Deady talked with me about his strategy for expansion at the company, which specializes in proprietary wireless real-time location system for tracking equipment and supplies in hospitals and other health care facilities. Deady, who has been working to raise another round of venture capital, has moved to diversify Awarepoint’s products and has beefed up the company’s sales reps and account managers.

—Cambridge, MA-based Vertex Pharmaceuticals (NASDAQ: [[VRTX]]), which has substantial operations in San Diego, agreed to pay $60 million upfront, and as much as $1.46 billion in follow-on payments to license new hepatitis C drug candidates from South San Francisco-based Alios Biopharma. I got a note from the Latham Watkins law firm, which was involved in the deal, that says: “This is the largest partnering deal Latham has ever done, the largest preclinical deal in history, the largest [hepatitis C] deal in history, and one of the 5 largest deals overall in biotech history. Had the full economics been announced, it would have been the largest biotech deal ever.”

—Luke’s BioBeat column argued that Twitter has become too useful for biotech executives to ignore anymore, and I think the same argument could be made for executives in other industries as well. As Luke put it: “I’ve been careful to follow people that have valuable and relevant information to report and share, while unfollowing everything else. I’ve expanded my professional network around the world by having conversations with readers I never would have met any other way. I’ve gotten story tips. And this is all happening even while … Next Page »

Comments | Reprints | Share:          

When I profiled Torrey Path in 2009, CEO Peter Dresslar was in the process of moving his software analytics startup from Ann Arbor, MI, to San Diego. The company was focused on providing information services to life sciences companies, and had developed the capability to provide a scientist or research group with all the data results from experiments involving a particular gene.

Dresslar tells me he’s now winding down Torrey Path to start a new company with Derren Barken, a bioinformatics scientist who was most recently at San Diego’s Prometheus Laboratories. Prometheus agreed last month to a buyout offer from Nestlé Health Science that one analyst has estimated to be worth more than $1 billion.

Torrey Path “generated a real amount of revenue and some assets,” Dresslar says. But the focus on a still-emerging field like genomics meant the company “was always running into headwinds” as the company’s customers struggled to advance both the science and the business. Dresslar says he’s now in talks to sell some of Torrey Path’s assets.

Dresslar, who is president of Sequencethree, says he got to know Barken through San Diego’s analytics software community and a local bioinformatics user group. The idea for starting a new bioinformatics startup came to them a couple months ago with “the realization that we wanted to work together,” Dresslar says. Their startup is initially focusing on complex problems in immunology. The two founders are developing computational technology to analyze the immunological properties of peptides and similar molecules, and Dresslar says they can envision ways to develop both new therapeutics and prophylactic vaccines from computer-based simulations.

“The technology takes advantage of massively parallel computing as well as some modern artificial intelligence concepts, and gives us a unique way of exploring complex biological phenomena related to those molecules,” Dresslar says. “We are exploring both technology licensing and developing our own intellectual property as possible commercialization paths.”

Barken is the director of bioinformatics at Sequencethree. He holds a doctorate in bioinformatics from UC San Diego and was a software developer at UCSD’s San Diego Supercomputer Center before he joined Prometheus Labs in 2007. His brother Lee is known among San Diego’s startup community as a CPA and IT practice leader at Haskell & White, and as a Cleantech San Diego board member.

“It’s just the two of us, although we have a couple of great advisors we’re going to be announcing in coming weeks,” Dresslar says. The founders have funded the company themselves so far, although Dresslar says they are looking at a combination of revenue-generating partnership activity, grants, and possibly an angel round in the next six to twelve months.

“We think we have a combination of technology and an approach that will let us understand the properties of biologically interesting molecules better than has been done previously,” Dresslar says. The co-founders also have been seeking out partnerships in fields besides immunology, because their approach also should work with a large number of other molecules. Dresslar says they can envision specific applications in analyzing anti-microbial peptide activity and even microRNA analysis.

Comments | Reprints | Share:          

Geospiza has been around the block a time or two in the bioinformatics business, and now after 14 years in the game, it has come to the end of the road.

The Seattle-based company, which makes software for scientists who analyze data from genetic experiments, said today it has agreed to be acquired by Waltham, MA-based PerkinElmer (NYSE: PKI), the giant maker of tools for life scientists. PerkinElmer, which said it generated $448 million in first-quarter revenue, didn’t disclose to investors how much it paid to obtain Geospiza. PerkinElmer CEO Rob Friel, however, did say in a conference call with analysts that the acquisition will have “minimal impact” on his company’s near-term finances, but that it represents a strong growth opportunity.

“Genomic information is becoming increasingly important in understanding and treating disease. Making sense of the unprecedented volumes of data generated by next generation sequencing and other biological measurements is critical to improve the disease diagnosis process and drug discovery,” said Richard Begley, PerkinElmer’s president of emerging technologies, in a statement.

Geospiza, which I profiled about a year ago when it turned profitable, has been one of the small and persistent voices in the market that has insisted that biologists need better software to manage genomic information. The company, founded in 1997, struggled to get traction with this argument in the wake of the Human Genome Project, but was able to weather the storm as competitors fell by the wayside, and the market eventually became more attractive. As DNA sequencing instruments from Illumina (NASDAQ: ILMN) and Life Technologies (NASDAQ: LIFE) have made it possible to sequence an entire human genome for as little as $10,000 and in a few weeks, it has created a tidal wave of DNA data points that more researchers are struggling to visualize and analyze.

Geospiza has long been forced to compete with old-school Excel spreadsheets in some cases, and custom-made “home-brew” software programs that individual biology labs make for their own projects. But Geospiza has gradually been chipping away at the market, winning over a series of big-name customers at places like the Institute for Systems Biology and University of Washington, Harvard Medical School, Yale University, Children’s Hospital Boston, and the University of Florida. Geospiza, as of a year ago, had about 20 employees.

It certainly looks like this deal has been brewing for a while. PerkinElmer took a multi-year license to Geospiza’s technology back in January.

Comments (2) | Reprints | Share:          

What do science, culture, and policy have in common? In order to improve the quality and affordability of health care, all three have to change. This message is central to Sage Bionetworks‘ mission and the theme from this year’s Sage Commons Congress held April 15th and 16th in San Francisco.

What’s the problem?

Biology is complex. This complexity makes it difficult to understand why some people are healthy and why others get sick. In some cases we have a clear understanding of the biochemical origins of health conditions and their treatments. Unfortunately, most drugs are effective for only a fraction of the people they treat, and in the cases where drugs are effective, their effectiveness is diminished by side effects. The most striking problems being adverse events, which are the sixth leading cause of death in the U.S.

One way to cost effectively improve health care is to increase the efficacy of treatments in greater numbers of individuals. Also referred to as personalized medicine, the idea is that future treatments are accompanied by diagnostic tests that indicate the treatment’s effectiveness. Accomplishing this goal requires that we understand the ways in which drugs affect their specific and non-specific targets with much higher precision. We also need to understand each target’s role in its biological pathway. However, as we attempt to break systems down into pathways and their component parts, a problem emerges. The components participate in multiple pathways and pathways interact with other pathways to form higher-ordered networks, and these interactions vary within individuals.

When visualized, biological networks look a lot like LinkedIn, Facebook, or Twitter networks. In these social networks, individuals participate in many groups and have connections to one another. Unlike social networks, which are easy to dissect, our biological networks comprise millions of interactions between proteins, DNA, RNA, chemicals, and microorganisms. Studying these networks requires advanced data collection technologies, computer programs, software systems, and social interactions. Therein lies the rub.

More data isn’t enough

Turning the vision of personalized therapies into reality requires a large numbers of scientists who understand the power of global analyses and can work together in research communities. Hence, one part of the Sage mission is to get greater numbers of scientists to adopt new approaches. Another part is getting them to share their data in useful ways.

Accomplishing this goal requires changing the research culture from one that emphasizes individual contributions to one that promotes group participation. Our publish or perish paradigm, combined with publication business models, discourages open-access and data sharing. It also reduces innovation. According to data presented by Aled Edwards, when faced with the opportunity to look at something completely new, we focus on well-known research problems. Why? Because funding is conservative and doing the same thing as your peers has less risk.

Bottom line, we need to take more risk in our research and take more risk sharing data pre and post publication. Taking more risk means we need to trust each other more.

Simply increasing data availability, however, is not enough. We also need to change … Next Page »

Comments (2) | Reprints | Share:          

The state budget being hashed out in Olympia is spreading angst far and wide, and you can bet Washington state’s biotech community will feel it this time.

The Life Sciences Discovery Fund, the program championed by Gov. Chris Gregoire to foster more biotech innovations and jobs in Washington, is being primed for what looks like another round of deep cuts. The fund’s executive director, Lee Huntsman, says that while Gregoire’s budget proposal in December included $27 million this year for the state biotech financing operation, the House proposed budget has zero money allocated for it, and the newly released Senate version sets aside $10 million.

No matter what the final number ends up being when the negotiating is done, it’s going to be a lot less than the $35 million annual figure that was projected when the Life Sciences Discovery Fund got up and running three years ago. The fund is supported by bonus payments that Washington gets for having played a lead role in the 1998 legal landmark settlement between states and tobacco companies. The vision for the Life Sciences Discovery Fund, which Gregoire pushed hard for, was to spend $350 million over 10 years on R&D projects that could have an impact on healthcare, and foster economic growth in the state.

The actual spending hasn’t lived up to the original projections. The Life Sciences Discovery Fund took a 41 percent cut in April 2009. That was when lawmakers were struggling with a $9 billion budget shortfall over a two-year cycle. This time, the state is said to have a $5 billion budget hole in the two-year spending plan, which is prompting lawmakers, again, to propose lots of unpopular things, like reduced support for higher education and pay cuts for state employees and teachers.

Lee Huntsman

Huntsman says he has been to Olympia several times lately to talk with lawmakers about the Life Sciences Discovery Fund, and how it is doing. The agency has made a number of investments in interesting projects for vaccines, genomics, and open source biology, but the report card at this point could best be described as incomplete. Huntsman has been emphasizing that the researchers who win Discovery Fund grants go on to leverage that with lots of extra support from the federal government and foundations, so this isn’t a case of the state propping up some dead-end ideas.

Maybe it was just getting to be a long day when we spoke on the phone, but Huntsman sounded a little weary of reciting the same old lines defending his agency’s existence. The Life Sciences Discovery Fund, he says, “was a good idea. It has worked out really well. It would sure be cool to continue, because it provides a lot of health benefit, and economic benefit.”

Comments (1) | Reprints | Share:          

San Diego’s life sciences community took two steps forward last week, as two new startups stepped into the light with new medical device technologies, and then one step back with the closure of another company founded in 2000. We have all the latest moves for you, plus a lot more.

—San Diego’s Topera Medical, which has maintained a low profile since it was launched three years ago, established a Lexington, MA-headquarters to commercialize technology developed by UC San Diego cardiologist Sanjiv Narayan. Topera, which hired former Boston Scientific executive Edward Kerslake as CEO, has technology designed to map the heart’s abnormal electrical currents, which occur with irregular heartbeats like atrial fibrillation.

—San Diego-based OncoSec, which was created March 1 through a reverse merger with a dormant public company, says it has licensed drug delivery technology from Innovio Pharmaceuticals to improve the efficacy of certain anti-cancer drugs. Inovio’s electroporation technology uses brief pulses of electricity to temporarily increase the permeability of cell walls, making it easier for OncoSec’s conventional chemotherapy drugs to penetrate cancerous tumors.

—San Diego’s Novalar Pharmaceuticals sold its only product, an FDA-approved drug for reversing the numbing effects of dental anesthesia, and will shut down in coming weeks. The French dental medication company Septodont acquired … Next Page »

Comments | Reprints | Share:          

San Diego’s Accelrys (NASDAQ: ACCL), which recently outlined its revised strategy for me, has signed a partnership agreement with Oxford Nanopore Technologies to develop software that will make it possible to get real-time analyses of experimental data from Oxford’s single molecule analysis system. Accelrys says its Next Generation Sequencing (NGS) technology for Pipeline Pilot uses a number of algorithmic, data management, and visualization components that scientists can quickly pull together with an easy-to-use, drag-and-drop visual programming environment.

Comments | Reprints | Share:          

Eight months after San Diego’s Accelrys (NASDAQ: ACCL) completed its merger with Santa Clara, CA-based Symyx Technologies, the scientific software developer is today lifting the curtain on a new strategy based on the company’s broader and deeper resources.

The merger, valued last year at about $175 million, combined Accelrys’ flagship software for simulating and modeling scientific experiments with Symyx’ strength in cheminformatics and notebook software used to chart and manage lab experiments. Along with its fourth-quarter financial results today, Accelrys is also sharing some new software products that are intended to help manage the entire process of scientific development—from R&D to commercialization and manufacturing—at industry, academic, and government institutions.

Max Carnecchia

“It’s the future for us, the strategy for the next two to three years,” says Accelrys CEO Max Carnecchia. “What we’re hearing from our largest customers is that they really need a framework, they need a [software] architecture that can harness all of the innovation, all the experiments, all the modeling and simulation, and all the work they’re doing across labs on a global basis, both within their own organizations and within their collaborators.”

In explaining today’s new product introductions, Carnecchia said, “A series of individual islands of capabilities have now been brought together into a true platform.”

The Symyx merger brought Accelrys a combined base of more than 1,350 customers, including 29 of the top 30 biopharmaceutical companies, all five top chemical giants, and many U.S. government agencies and universities.

“It was actually our customers who talked with us about their needs during the merger and pre-merger” that led to the strategy, says Melissa Purcell, Accelrys’ senior director of marketing communications.

“Obviously, we had thoughts around the idea that the combination was going to create … Next Page »

Comments (3) | Reprints | Share:          

If your name is Borya Shakhnovich, people tend to make assumptions about you. One, they don’t want to play you in competitive chess. Two, they wouldn’t be terribly surprised if you introduced yourself by saying something like, “I am scientist.”

OK, I’m stereotyping here (a real time-saver, I know), but at least one of those assumptions has some basis in fact. Shakhnovich is the founder and CEO of Brookline, MA-based iAMscientist, a global community and resource site for researchers and institutions in science, technology, and medicine. He has raised $1 million in seed financing from angel investors including George Whitesides, the famed Harvard University chemist and co-founder of more than a dozen companies including Genzyme (which was acquired last week by Sanofi-Aventis for some $20 billion).

What iAMscientist does is give researchers and institutions some interesting new tools to connect with each other. The idea is to create an online community and directory of top-tier people so that research teams, companies, and other organizations can find the right person to answer a difficult question, decipher a new paper, or lead a research project. All of this is especially important for interdisciplinary ventures—like when biologists team up with physicists, computer scientists, or electrical engineers to model things like genetic pathways or disease mechanisms, and then someone wants to commercialize the findings.

“We provide an organization with the ability to find that one person who is the foremost expert in an obscure area—our value is in that matching mechanism,” Shakhnovich says. Some of the most valuable knowledge and experience that researchers have “isn’t really in their papers, it’s in their heads,” he says. “You want to get in touch with them and maintain a relationship.”

Academic social networks are not new, of course. Services like Academia.edu, Epernicus (Boston-based), Labmeeting (founded by a Harvard grad), Nature Network, Pronetos, ResearchGate (which started in Boston but recently moved to Germany), and, to some extent, LinkedIn, all help … Next Page »

Comments (2) | Reprints | Share:          

Genomic Health built itself into a profitable business in molecular diagnostics by using genetics analysis instruments that were state-of-the-art in the middle part of the last decade. But as the Redwood City, CA-based diagnostics company (NASDAQ: GHDX) looks further into the future, it has come to a clear conclusion.

Out with the old, and in with the new.

Genomic Health is looking for a way to rekindle its rapid growth of the past few years, and betting on new technology is a big part of the strategy. The company said last week it generated $178 million in sales in 2010, and achieved its first full-year profit since it was founded in 2000. But investors didn’t see much to cheer about here, because revenue grew only 19 percent over the prior year, and the company forecasts are that growth will level off at around 12 percent to 18 percent growth next year. Wall Street sent the stock down 5 percent the next day.

Certainly, Genomic Health has short-term things it can do to maximize its bread-and-butter Oncotype DX test by expanding into international markets, and by branching beyond breast cancer into colon and prostate tumor tests. But as those products run their course over time, Genomic Health wants to be in position to roll out new tests based on the breakneck pace of innovation of the past couple years in fast/cheap gene sequencing. So it’s investing in new diagnostic tests will look for patterns in a lot more genes than today’s molecular diagnostics can, and will make discovery of new tests cheaper, says founder and executive chairman Randy Scott. The spending is a drag on Genomic Health’s financial performance today, but the bet is it will pay big dividends further in the future.

“We are heavily invested in R&D programs, like next-gen sequencing, that are going to impact our bottom line for the next five years,” Scott says. “But we think it will help us build this eventually into a multi-billion dollar business over the course of the next 10 years.”

You need to dive a little bit into the history of technology at Genomic Health to understand what’s going on here. The company developed its first Oncotype DX test based on an instrument known as a real-time PCR machine, which uses the TaqMan chemistry sold by Life Technologies’ Applied Biosystems unit. The instrument, which amplifies DNA samples for analysis, was used to help discover the original 21-gene signature that Genomic Health’s Oncotype DX uses to predict the chance a woman with breast cancer will relapse, and whether she will benefit from a round of preventive chemotherapy. The RT-PCR platform was the best choice at the time, Scott says, because it had “really exquisite sensitivity, reproducibility, and precision.” The machine has been so good on those parameters, Genomic Health continues to use it for running the commercial tests it performs today.

But the more genes you want to analyze, the more expensive real-time PCR becomes. To recoup its sizable investment, Genomic Health to set a price of $4,000 for its one-time test, which has forced the company to run a lot of health economic analyses to justify the price. And as the company began to reach the limits of PCR technology, it started looking for a replacement platform, Scott says.

Given that several companies are now talking about sequencing entire genomes for $10,000 today, and potentially $1,000 or less in the not so distant future, it shouldn’t be a surprise that a company like Genomic Health is particularly interested. Over the past year, Genomic Health has been switching over its discovery research work to the new fast/cheap sequencing machines … Next Page »

Comments (1) | Reprints | Share:          

Writing about business at the microscopic level of genes and cells means that I rarely get to see compelling A/V shows of products in action. So last night was a rare treat to get an up-close look at a half dozen fun and interesting startups in Seattle, from a variety of industries, who were asked to give 8-minute demos that would do no less than make a business audience fall in love with their product.

This was the scene at the Northwest Startup Demo event at One Union Square in Seattle, organized by the MIT Enterprise Forum of the Northwest. I served as one of seven judges who were asked to award the prize for the best product demo. This was my first time judging this competition, but I will say that the overall quality of presentations struck me as surprisingly good, and there may even be a couple companies with legs. Kent, WA-based LaserMotive, the sci-fi-like company that beams power wirelessly, walked away with the top prize of the evening, but in my view, this was a close call.

“This year was the best we’ve ever had in terms of overall quality,” said Villette Nolon, president of Seraph Capital Forum, and a more seasoned judge than I.

Here are some brief highlights from each of the finalists who presented their demos:

—EverSpeech. This Redmond, WA-based company, led by Charles Hemphill, offers speech recognition technology to help professionals fill out forms on the Web. Hemphill wore a noise-reducing headset, speaking clearly into his microphone, and showed on a screen how he could quickly and easily fill out an engineering inspection form without using his hands. One example he gave, to illustrate how it works, was of how an airplane mechanic who’s up on a ladder looking at parts could fill out a form without having to use his hands to jot notes.

—Lipp Sync Automotive. Entrepreneur Bob Lipp had the audience giggling from the get-go with his demo. He fired up a program on his computer to demonstrate what he calls the “Throttlebox,” which he intends to sell to hybrid car owners as a way to simulate engine noise at low speeds, to help avoid accidents that can happen by running into unsuspecting bicyclists and pedestrians. The funny thing was the sound—the engine he was simulating was that of a growling V-8 from a 1970 Ford Mustang at idle—not exactly the kind of sound people envision coming from a Toyota Prius.

You can laugh all you want, but Lipp made his case … Next Page »

Comments (3) | Reprints | Share:          

Bioinformatics was a buzzword at the beginning of the genomic era about a decade ago, but it has become a dirty word today. It’s sort of like shorthand for a highly fragmented cottage industry that seeks to analyze biological data, in which no one seems to make money. But whatever you want to call it, Saeid Akhtari still sees big opportunity in using information technology to help biologists make sense of all the genomic data piling up in servers around the world.

And he’s actually starting to make money at it.

Akhtari’s company, Cupertino, CA-based NextBio, doesn’t claim to have singlehandedly solved all the data overload issues that are emerging as genomic instrument makers race ahead with machines that seek to sequence complete human genomes, with 6 billion chemical letters, for $5,000 or even less in coming years. But NextBio has grown to 60 employees, built up an impressive roster of blue-chip pharmaceutical and academic customers, and has started to operate on a cash-flow positive basis in its sixth year, Akhtari says.

The big idea at NextBio is to take the vast amounts of genomic data piling up in free public databases like those run by the National Institutes of Health and pool it with proprietary internal data from for-profit customers, in a way that can be mined by average lab bench researchers in real-time. NextBio’s vision is to make this web-based service so easy to use that a biologist doesn’t need help from a trained bioinformatics expert, and can get clear answers that shed light on how, say, certain genes are up-regulated or down-regulated in a diseased tissue.

“We’re finding that by correlating different pieces of data, new things pop out at you,” Akhtari says.

Saeid Akhtari

NextBio got started back in 2004. That was when Akhtari sold his last bioinformatics company, Silicon Genetics, to Agilent Technologies for an undisclosed sum. Akhtari co-founded the new venture with Ilya Kupershmidt, one of his key lieutenants at Silicon Genetics, and Mostafa Ronaghi, the chief technology officer of the market leader in gene sequencing instruments, San Diego-based Illumina (NASDAQ: ILMN).

Back then, NextBio saw the growth in genome-wide association studies, the search for subtle variations in genomic code called single nucleotide polymorphisms (SNPs), and the growing use of next-generation sequencing tools that were making it possible for biologists to run all kinds of new experiments that might shed light on what’s going wrong and causing disease. One of the big problems then, Akhtari says, was that biologists couldn’t just run queries against these datasets on their own—they needed to ask for help from a bioinformatics expert. It was sort of like the days before Google or Bing, when information professionals needed to ask research librarians trained in Boolean logic to run online queries that got good results. The simple numbers game says … Next Page »

Comments | Reprints | Share:          

One huge story hit Seattle biotech this week. I got all the usual “who, what, when, where” in the initial reports. But I’m still thinking hard about the nuances of why this happened, and what will come next. Stay tuned.

—The big news, of course, came when Bristol-Myers Squibb said it has agreed to acquire Seattle-based ZymoGenetics (NASDAQ: ZGEN) for $885 million, or $9.75 a share. This represents the end of the road for Seattle’s oldest independent biotech company, one that once dreamed big about being the anchor of the Northwest life sciences cluster. The initial word from a ZymoGenetics spokeswoman was that a lot of people would likely lose their jobs in the transaction, although ZymoGenetics CEO Doug Williams later insisted that “no decisions have been made” about local job cuts, and that he will personally advocate that Bristol retain many of the talented people in the Zymo workforce over the next couple months. But the financial offer is likely too good for shareholders to turn down (an 84 percent premium over the prior’s days closing stock price), so this deal looks like a slam dunk. We will be watching closely what really happens to Zymo’s 320 employees, and the local biotech community, in the aftermath of this deal.

—Stratos Genomics, a stealthy Seattle company looking to enter the competitive field of low-cost gene sequencing, said this week it has closed a $4 million Series A venture round.

—Swedish Medical Center said this week it has named Dr. Mark Reisman, the well-known interventional cardiologist, to be its new chief scientific officer and head of research. This is part of an amped-up research effort at the Seattle hospital, in which it will also focus on “adopting new and emerging therapies as well as acquiring the latest technologies, faster.”

—Insilicos, the Seattle developer of biomedical software and diagnostics, said it has received a $1.2 million grant from the National Institutes of Health to predict heart attack risk in patients with cardiovascular disease. The study will examine 400 patients at the University of Washington.

—Emerald BioStructures, the Bainbridge Island, WA-based contract research firm, said it has formed a new collaboration with Boulder, CO-based SomaLogic to determine precise crystal structures of protein targets on cells. Financial terms weren’t disclosed.

—This feature ran more than a week ago, but I was out on vacation then, and thought I’d include it today for readers who might have missed it. It’s the story of Seattle Children’s CEO Tom Hansen, and how he has led a team at Children’s that has developed what could be a simpler, more effective, and far cheaper ventilator to keep premature infants alive in the developing world.

—We showcased a couple new guest writers in the op-ed section of Xconomy Seattle this week. Shawn Iadonato, the chief scientific officer of Seattle-based Kineta, offered up his opinion that the federal government ought to start supporting early-stage drug development, not just academic research. And Jodie Spitze, a science teacher at Kent-Meridian High School, made a case for why high school educators need to get serious about bioinformatics if they want to prepare young people for a promising field of study in the future.

—Lastly, sharp-eyed followers of the Xconomy Seattle event calendar and my Twitter followers may have noticed I quietly added a new kind of event here which we are calling “Xconomy Meetup.” This is a free and open conversation with readers at a local watering hole, featuring one special guest each time we do this (probably once a month). The first guest is Carl Weissman, the OVP managing director and Accelerator CEO. You can bet the subject of ZymoGenetics will come up early and often. So come on over to the Streamline Tavern in Lower Queen Anne sometime from 4:30 pm to 6:30 pm on Monday and chat with me and Carl and other readers who want to join the conversation.

Comments | Reprints | Share:          

We covered a variety of subjects on the biotech beat this week—cloud computing for genomics, a new idea for bioinformatics, an environmental health startup co-founded by Corey Goodman, and a profile of the new CEO of BayBio. Read on to catch up on the week’s headlines.

—Gail Maderis has spent a career working up the executive ranks of biotech at Genzyme and Five Prime Therapeutics, and now she says it’s her time to give back as the CEO of BayBio.

—Calithera is the latest startup to emerge from the UC San Francisco lab of Jim Wells, a longtime scientist from Genentech and the founder of Sunesis Pharmaceuticals. Calithera has raised $40 million in venture capital, including some from the new Mission Bay Capital fund, to develop a new class of cancer drugs.

—Genentech, the U.S.-based unit of Roche, said this week it has filed an application with the FDA for clearance to start selling T-DM1, the souped-up antibody drug for breast cancer. I wrote an in-depth feature about this drug on the day we launched Xconomy San Francisco last month.

—Amazon (NASDAQ: AMZN), the Seattle-based online retail giant, is starting to see genomic researchers adopt its cloud computing service to help manage the massive amounts of data as gene sequencing gets much faster and cheaper.

—DNAnexus, a Palo Alto, CA-based startup, is seeking to build on Amazon’s cloud computing infrastructure to become the leader in bioinformatics, which all about making software to help genomic researchers analyze and visualize all the new sequencing data.

—iPierian, the South San Francisco-based developer of stem cell technology for drug discovery, said it has raised a $22 million Series B venture round, led by Google Ventures. The company also is making a leadership switch, as Michael Venuti is replacing John Walker as CEO.

—Corey Goodman is known as a medical biotech entrepreneur, but now he’s making his first foray into an environmental health startup. The new company, PhyloTech, told me about its plans in this in-depth feature.

—Ingenuity Systems, the Redwood City, CA-based company that offers search capabilities to life scientists, has secured $15.3 million in new equity financing, according to a regulatory filing. We also spotted a $13.2 million financing in the regulatory filings from Invuity, a San Francisco-based startup with technology to help surgeons better visualize what they are doing.

—Lastly, we had a notable guest editorial relevant to the life sciences. Joseph Jackson talked about “The Open Science Shift” in a thought-provoking post in advance of a big meeting in Berkeley he’s preparing for July 29-31.

Comments | Reprints | Share:          

The time is right for someone to come along and build a great company in bioinformatics, according to Andreas Sundquist. He’s betting it will be his team at Palo Alto, CA-based DNAnexus.

Scientists have been complaining for years about massive amounts of data piling up on their servers as gene sequencing instruments have become ever better, faster, and more efficient. Yet even as San Diego-based Illumina built a business worth $5 billion as the market leader in these instruments and the chemical reagents they need, nobody has come along with a dominant software program to help researchers analyze and visualize what these billions of genomic data points mean for human health.

Sundquist, 30, has seen the data logjam get worse through his years in graduate school. He was 23 and just embarking on his career in computational biology when the original Human Genome Project was completed in 2003. He studied computer science and electrical engineering at MIT, and then went on to get his doctorate in computational biology from Stanford five years later. Those years were marked by extraordinary progress from companies like Illumina and Life Technologies that have brought the cost of sequencing below $10,000. One ambitious startup, Menlo Park, CA-based Pacific Biosciences, is racing to make a machine that can perform the task in as little as 15 minutes.

While all that innovation was happening, Sundquist and his peers at Stanford saw the software to analyze all this data is still produced by a cottage industry. The bioinformatics industry is mainly composed of custom-made programs at individual labs, with some open source programs, and a few small private companies like Seattle-based Geospiza and Westborough, MA-based GenomeQuest. The market is still tiny, probably in the “tens of millions” of dollars, Sundquist says. But it is bound to become more lucrative over time as fast, cheap sequencing becomes the norm and researchers will have to better analyze their data to delve deeper into what genomes can tell us about human health and disease.

Andreas Sundquist

“We saw a huge trend,” Sundquist says. “We believe there’s going to be a large market in sequence analysis.”

DNAnexus got going last July with a $1.55 million seed financing, led by First Round Capital out of San Francisco. Sundquist was joined by a pair of co-founders from the Stanford faculty—Arend Sidow, an associate professor of pathology and genetics, and Serafim Batzoglou, an associate professor of computer science. The company debuted with its commercial product in April at the Bio-IT World conference in Boston, and has signed up “hundreds” of users since, Sundquist says.

The idea at DNAnexus is to offer a low-cost, user-friendly way for researchers to do some basic analysis of their sequencing runs. Typically, a researcher will run a sequencing instrument to get the data he or she wants, and then spend six to 12 months “playing around with the data,” Sundquist says. That means finding out what tools are available, downloading them, and figuring out how … Next Page »

Comments | Reprints | Share:          

The future of biology, if Amazon has its way, will be in the cloud.

The Seattle-based online retailer (NASDAQ: AMZN) has generated buzz the past few years with its foray into cloud computing through Amazon Web Services. This is the model in which customers rent server space on a pay-as-you-go basis, and get access to their data anytime via the Internet. It’s supposed to allow small businesses, governments, and anybody else to save cash and hassles by not having to buy and maintain their own in-house servers. The model is credited with enabling a new generation of lean tech startups to build businesses using far less capital.

Biological researchers haven’t embraced the new model as quickly as their tech brethren, but the cloud computing wave is coming to life sciences, says one of Amazon’s biotech liaisons, Deepak Singh. The trend is coming out of necessity. Gene sequencing has been on a breakneck pace of innovation over the past few years, as instrument makers like San Diego-based Illumina and Carlsbad, CA-based Life Technologies have lowered the cost of sequencing an entire human genome to as little as $10,000. Upstarts like Mountain View, CA-based Complete Genomics seek to sequence entire genomes for as little as $5,000, while a rival, Pacific Biosciences, is aiming to sequence genomes in 15 minutes. Since every human genome has 6 billion chemical units of DNA, this faster and cheaper form of sequencing is creating enormous datasets that somebody will need to store, analyze, compare, and visualize. Without that capability, it’s just a vast pile of data that doesn’t really lead to valuable new insights for medicine.

Computing challenges have become a “serious blocker” to people trying to make sense of the genomic wave, Singh says. And Amazon has made it a high priority over the past couple years to become the company that stores genomic data in a cheaper and more accessible way for researchers. Customers, Singh says, “have started looking at the cloud very seriously as a possible option. Over the last year or so, that curiosity has turned into serious adoption.”

Amazon‘s pay-as-you-go, rented server model has attracted partners and customers all over the country. The Broad Institute of MIT and Harvard in Cambridge, MA, is a user, along with Harvard Medical School. Life Technologies, an instrument maker, and Seattle-based Geospiza, a bioinformatics software company, have a partnership to use Amazon’s servers to store genomic data. Palo Alto, CA-based DNAnexus, an intriguing bioinformatics startup, has built its business model around using Amazon Web Services. And one of the leading evangelists for cloud computing in genomic research is C. Titus Brown, a computer science and microbiology professor at Michigan State University, who is teaching students how to use Amazon Web Services to store the data for their experiments.

Precisely how important this is to Amazon, a company with $24.5 billion in revenue in 2009, is hard to say. In keeping with Amazon’s close-to-the-vest culture, Singh would only offer vague adjectives when I asked for specifics on the number of customers, the percentage of Amazon Web Services business that comes from life sciences customers, the number of employees devoted to this effort, and the size of the market that Amazon ultimately sees for cloud computing services in life sciences.

There are still major barriers to be cleared before … Next Page »

Comments (8) | Reprints | Share:          

San Diego’s role in computer analytics dates back to at least 1969, with the founding of Science Applications Inc., now SAIC, which used computer models to predict the effects of nuclear blasts for the Government. Today, a life sciences industry that didn’t exist in San Diego 40 years ago is embracing increasingly powerful computational tools to make sense of the massive amounts of data resulting from genetic discoveries and advances in molecular profiling.

Among the leaders in this emerging field is Paul A. Rejto, director of computational biology in oncology research at Pfizer in San Diego. A physical and theoretical chemist, Rejto started in 1994 at Agouron Pharmaceuticals, a San Diego biotech that became part of Pfizer in 2000. We caught up with Rejto by e-mail last week to find out more about the technology, its role in pharmaceutical research, and its importance to San Diego.

Xconomy: What is computational biology?

Paul Rejto: As with many interdisciplinary fields, there is no single well-established definition. Computational biology broadly refers to the application of computational and informatics approaches to address questions in biology. A number of other terms describe activities at this interface, with slightly different flavors. Bioinformatics is typically more focused on algorithms for sequence manipulation and analysis, and biomedical informatics is more focused on the acquisition and analysis of patient data and outcome.

X: What are some applications of computational biology?

PR: As you might imagine there are many applications. Here in the Pfizer Oncology Research Unit, we are applying computational approaches to support two major objectives: 1) identification and credentialing (or validation) of oncology targets, and 2) linking targets to patients using predictive markers of response. Our chief scientific officer, Neil Gibson, refers to these efforts as the bookends of the research portfolio – in other words, we support the selection of projects that are initiated within research and help to ensure a successful path for those projects moving forward out of research into the clinic.

To credential new targets, we use genomics and transcriptomics to assess targets and pathways in well-defined populations with unmet medical need, and look for evidence of functional activation. To accomplish this, we work closely with our commercial colleagues to ensure … Next Page »

Comments | Reprints | Share: