Cypher Genomics

Cypher Genomics

Cypher Genomics has developed software to rapidly analyze billions of gigabases of genome sequencing data and identify the genetic variations that are most relevant to a patient’s disease or disorder. In the case of Lilly Grossman (pictured), a teenager with severe, undiagnosed muscle tremors, Cyper's technology rapidly identified specific genetic mutations in two genes---and pointed the way to the best available therapy. The startup was founded in 2011 by four prominent researchers at the Scripps Translational Science Institute, and now has 15 employees. Angel investors have privately funded operations so far, and former Gen-Probe chairman and CEO Hank Nordoff is executive chairman.

GovX

GovX

GovX operates an e-commerce website for the exclusive use of current and retired military and government employees. Members qualified by the company's online verification technology can purchase premium lifestyle products and gear at a discount, directly from manufacturers. GovX was founded in 2011 by Marc and Shannon Van Buskirk (who had created a similar online channel acquired by Oakley) and Tony Farwell. The startup now has about 60 employees and has raised a total of $21 million from Alestra Ltd., Arbor Group, and angel investors.

Dealstruck

Dealstruck

Dealstruck is a Web-based direct lender founded in 2012 by entrepreneurs Russell McLoughlin (left) and Ethan Senturia. The fintech startp provides term loans and lines of credit to small business owners. Dealstruck says it has lent more than $80 million in just 18 months, and is on track to double in size over the next year. The startup has about 53 full-time employees and has raised about $15 million from investors (led by Trinity Ventures), and $85 million in debt, led by Brevet Capital Management.

Seismic

Seismic

Seismic provides Software-as-a-Service to manage and support sales and marketing teams. Seismic's LiveDoc technology allows marketers to revise information in one place, and it updates in every online document used by sales teams. Founded in 2010 by CEO Doug Winter, Nasser Barghouti, Ed Calnan, Marc Romano, Fred Xie, Seismic has raised $24.5 million from Jackson Square Ventures and JMI Equity, and has 105 full-time employees.

Cloudbeds

Cloudbeds

Cloudbeds has developed browser-based hospitality management software used by hotels in 115+ countries. Its SaaS platform helps independent hoteliers and hostel owners run their businesses. The startup was founded in 2012 by Adam Harris and Richard Castle, and employs over 50 people in San Diego, São Paulo, Brazil, and Dublin, Ireland. The company garnered $6.5 million through two rounds from investors David Kloeppel, Joe Maxwell, Moore Venture Partners, and Nashville Capital. Pictured: Milhouse Hostel, a Cloudbeds partner in Brazil.

StackIQ

StackIQ

StackIQ, founded in 2011 by (from left) Greg Bruno, Tim McIntire, and Mason Katz, specializes in software used to automate datacenters used by big companies, telcos, and cloud/hosting providers. StackIQ's technology has benefitted from the industry shift from three-tiered server farms (database, app server, and Web server) to flatter, but highly distributed server clusters. (OpenStack, Hadoop, Spark, are all examples of this trend.) So far, StackIQ has raised $10.5 million from Avalon Ventures, Anthem Venture Partners, Greyhawk Capital, and OurCrowd.

Nervana Systems

Nervana Systems

Nervana Systems provides "deep learning" technology as a cloud-based service. The company says its unfair advantage is making it easy for customers to use the latest machine intelligence technology. Nervana was founded in 2014 by Qualcomm expats Naveen Rao, Amir Khosrowshahi, and Arjun Bansal, and now has 30 full-time employees. It has raised a total of $25 million through several rounds. DFJ partner Steve Jurvetson and Data Collective partner Matt Ocko hold board seats.

Measurabl

Measurabl

Measurabl provdes Web-based software that building owners can use to measure and manage their energy costs. Earlier this year, Battery Ventures acquired Enviance, a Carlsbad, CA-company that developed similar SaaS tools for managing environmental, health, and safety regulations. Measurabl says it also can provide energy project financing, investment-grade certification, and market intelligence. The sustainability-focused startup was founded in 2013 by Matt Ellis and now has 11 employees. It has raised $2 million in venture financing from Crosscut Ventures with participation from several real estate industry veterans and Angel investors.

Photo courtesy BLINQ.

ScoreStream

ScoreStream

ScoreStream is a Web-based media startup focused on crowd-sourcing local sports news. ScoreStream's users can share the scores, photos, videos, and game chatter of more than 6,000 high school sporting events in real-time each week. ScoreStream was founded in 2012 by CEO Derrick Oien, and Joshua Stephens, David Podolsky, and Bruce Worman, and now has 12 employees. The Sinclair Broadcasting Group, Avalon Ventures, NEA, and the Under Armour CEO Kevin Plank have invested $3.1 million.

Classy

Classy

Classy is a cloud-based fundraising and community management platform built for use by schools, nonprofits, and other social impact organizations. CEO Scot Chisholm tells me that he and founders Pat Walsh, Marshall Peden, and Joe Callahan began fund-raising in 2006, but did not develop Classy's software platform until 2011. Angel investors provided initial funding until Classy got $18 million in a Series B round led by Mithril Capital Management that was joined by Salesforce Ventures, Bullpen Capital, Venture51, Galileo Partners, and Rethink Impact. (Interest in Classy has intensified since Accel Partners and Technology Crossover Ventures acquired a majority stake earlier this year in GoFundMe, another San Diego crowdfunding platform.)

CyberFlow Analytics

CyberFlow Analytics

CyberFlow Analytics was founded in 2013 by Hossein Eslambolchi (pictured), a former AT&T CIO and CTO; Tom Caldwell, a former Cisco Systems executive; and Louie Gasparini, a former CTO at RSA, the network security division of EMC. CyberFlow says its technology uses a combination of advanced clustering analytics, cyber intelligence, and big data visualization to thwart the type of sophisticated network attacks that organized crime and nation states are mounting these days. CyberFlow raised $4 million in seed funding from angel investors and two strategic partners, Toshiba and Siemens, and has begun work on a Series A financing round. The company has 15 employees and has generated over $1 million in revenue so far this year.

GoFormz

GoFormz

GoFormz says its mobile app and Software-as-a-Service technology lets business customers capture data electronically with mobile forms that look exactly like their existing paper forms. Data and documents are stored in the cloud, and can be accessed through GoFormz reports, API, or partners like Box. Founders Jonathan Freitas, Jonathan McIntire, Andrew Stevens, Jonathan Stevens, Jason Craven, and Jeff Fildey started the company in 2012, with undisclosed Series A funding from Cloud Apps Capital Partners and Floodgate. The company has 23 full-time employees.

Omniome

Omniome

Omniome was founded in 2013 by Kandaswamy "Swamy" Vijayan, who worked previously at San Diego-based Illumina. He has described himself as an "integration specialist in the next-generation sequencing area, with expertise in both platform and assay development." But the startup remains in stealth. (Note what's written on the nametag in this photo from the "technology" page of Omniome's website.) Silicon Valley's Data Collective (DCVC) identifies Omniome as a portfolio company.

Software is making a comeback in San Diego.

It’s not exactly a sea change. But there are more companies now, more investments—and investors—and more startup activity than there was even a few years ago, when a lack of direction in the tech sector here led to unflattering comparisons to the horse latitudes.

Some of San Diego’s stronger Web companies have raised substantial venture rounds. Tealium has taken in nearly $78 million in equity and debt to manage website metadata tags, and TakeLessons has garnered $20 million to operate an online marketplace for lifelong learning. Both were founded in 2008.

Since then, a whole new generation of software startups has taken root in San Diego. Many companies are already turning heads with impressive startup teams, significant early stage funding rounds, rapidly growing revenues or users—or a combination of those factors and more.

So the timing felt right for Xconomy to highlight a dozen or so of the most-promising tech startups to watch in San Diego.

We made our selection from companies that were screened by the San Diego Venture Group for its annual venture summit, which begins Thursday (tomorrow!) at the Manchester Grand Hyatt in downtown San Diego.

Over 160 startups from the San Diego area applied to participate in the annual venture summit, according to Mike Krenn, the venture group’s president. (Krenn and other members of the venture group selected 32 local companies from this pool to make presentations to 100+ venture investors in a private, invitation-only demo day.)

From the same pool of applicants, the venture group also named 40 startups as “cool companies,” and invited them to exhibit their technology Friday at the Manchester Grand Hyatt as more than 700 people gather for the venture summit’s main event, which is open to the public. The agenda includes presentations on Qualcomm’s robotics initiative, doing business in China, the business of cannabis and 2016 elections, and the convergence of chip design and genomics.

This year’s keynote speaker is Fred Wang of Trinity Ventures, which led venture rounds in two San Diego startups earlier this year—Cybersecurity startup Harvest.ai, which raised $2.3 million in March, and fintech startup Dealstruck, which took in $8.3 million in April.

“I’d like to think that’s a foreshadowing of greater things to come,” said Krenn. Getting an “A list” venture firm like Trinity from Silicon Valley’s fabled Sandhill Road to invest in two San Diego startups is “something I haven’t seen in a long time,” he added.

Other prominent venture investors with multiple deals in San Diego include DFJ, Avalon Ventures, Jackson Square Ventures (previously known as Sigma West), and Qualcomm Ventures. Some new angel investors also have been making multiple investments in recent years in San Diego, most notably Taner Halicioglu, a UC San Diego computer science grad who was one the first software developers hired at Facebook; Craig Lauer, a former Qualcomm engineering VP, and Allison Long Pettine, who invests in both technology and life sciences startups.

To add some mystery to our list, I’ve added a San Diego startup that is still in stealth mode to create a “baker’s dozen” of San Diego tech startups to watch. Omniome is an intriguing biomedical diagnostics company whose founder and CTO, Kandaswamy “Swamy” Vijayan, previously worked at Illumina (NASDAQ: ILMN), the San Diego-based leader in genome sequencing technology. Vijayan declined to comment for this article, saying the company is intent on remaining below the radar until it makes its debut in the first half of next year.

Omniome represents one of the hottest and most-compelling areas of innovation in San Diego, as the revolution in genome sequencing looks to the IT industry for solutions to the kind of problems that require sophisticated applications of Big Data and analytics. Cypher Genomics, which is also on our Xconomy list of tech startups to watch, has developed   software-as-a-service analytics that accurately interpret genomic data. Another San Diego early stage company, Edico Genome, is integrating software and hardware processing technologies to ease a data processing bottleneck in genome sequencing.

Omiome, from what we can tell, is part of this vanguard of San Diego startups at the convergence of Big Data and “Big Biology.” Omniome was admitted last June into San Diego’s EvoNexus incubator (which has hosted several companies on our list). In one of its few public disclosures, Omniome says it is developing low-cost biosensors that can be adopted for mobile diagnostics and health monitoring.

Yet it is worth noting that to genomic researchers, the “omniome” refers to a comprehensive database for storing information about the genomic sequences of bacteria. (Such a database might be useful, for example, in identifying bacterial DNA from a blood sample or biosensor data.) It’s also worth noting that Data Collective (DCVC), the Bay Area venture firm that specializes in big data startups, has made an undisclosed investment in Omniome (according to PitchBook data used by Entrepreneur magazine to identify the top early stage VC firms), and DCVC lists Omniome as a portfolio company on its website.

Bruce V. Bigelow is the editor of Xconomy San Diego. You can e-mail him at bbigelow@xconomy.com or call (619) 669-8788