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Achieves First Instrument Revenue and Significant Milestones

CAMBRIDGE, Mass., May 14, 2009 -- Helicos BioSciences Corporation (NASDAQ: HLCS) announced today its financial results for the quarter ended March 31, 2009.

"Entering the second quarter of 2009, we believe that the progress we made during 2008 and the first quarter of 2009 has positioned Helicos with a very competitive single molecule sequencing solution for 2009 and beyond." said Ronald A. Lowy, Helicos Chief Executive Officer. "The throughput and cost of ownership metrics of our Helicos(TM) Genetic Analysis System, coupled with the unique capability to accurately sequence and quantitate any genomic target, are strong examples of what distinguishes Helicos in the marketplace. We are also very pleased to record our first instrument product revenue during the first quarter of 2009 as we gain traction in the marketplace."

Q1 2009 Financial Results:

For the first quarter of 2009, the Company reported a net loss of approximately $6.5 million or $0.10 per share. This compares to a net loss of approximately $11.8 million or $0.57 per share for the first quarter of 2008. The Company ended the first quarter of 2009 with approximately $13.9 million in cash.

The Company reported approximately $1.2 million in revenue for the first quarter of 2009, which includes $963,000 in product revenue from the sale of an instrument that was shipped in 2008 and the sale of proprietary reagents to customers and $239,000 in grant revenue from the National Institutes of Health (NIH). For the comparable period in 2008, the Company reported total revenue of $113,000 which represents grant revenue from the NIH.

Total operating expenses for the first quarter of 2009 were approximately $7.5 million compared with $11.9 million for the first quarter of 2008. Total operating expenses for the first quarter of 2009 were down approximately $2.5 million on a sequential basis when compared with the fourth quarter of 2008 as a result of the Company's efforts to reduce its operating costs.

Operational Highlights:

Commercial

To date, Helicos has installed its Helicos(TM) Genetic Analysis System at three user sites and has received commitments for two additional installations which are expected to be made during the second quarter of 2009. Of these installations, two of the systems have been purchased by customers and three have been designated as reference site installations at institutions for scientific and commercial evaluation. Helicos expects that these installations will provide additional revenue from the sale of proprietary reagents and that the results of the system evaluations will lead to additional sales.

The current performance capability of Helicos' True Single Molecule Sequencing (tSMS)(TM) technology has generated a significant increase in the number of requests for quotes. In addition, Helicos' quoting activity has been further enhanced by the new funding opportunities from the National Institutes of Health as a result of the economic stimulus program. Helicos is actively working with customers on the design of grant proposals for funding research programs that will benefit from the HeliScope(TM) platform.

Helicos continues to provide various application datasets and methodologies using its True Single Molecule Sequencing (tSMS)(TM) technology. These datasets, which can be found at Helicos' HeliSphereTM Technology Center (), have resulted in expanded interest from potential customers. In addition, Helicos scientists, as well as outside users and collaborators, are submitting manuscripts to peer reviewed scientific journals for publication of data from recent sequencing projects using Helicos' tSMS(TM) approach.

System Performance

Based on continued improvements to the Company's single molecule sequencing platform, as of May 2009, the Helicos(TM) Genetic Analysis System has been shown to be capable of achieving the following sequencing performance metrics:
Throughput of up to 170 useable megabases per hour with DNA samples.

The resulting throughput and reads result in an average cost as low as 45 cents per megabase.

Technology and Science

About Helicos BioSciences:

Helicos BioSciences is a life science company focused on innovative genetic analysis technologies for the research, drug discovery, and diagnostic markets. Helicos' proprietary True Single Molecule Sequencing, tSMS(TM), technology allows direct measurement of billions of strands of DNA enabling scientists to perform experiments and ask questions never before possible. Helicos is a recipient of the $1,000 genome grant and committed to providing scientists the tools to unlock the era of genomic medicine. The company's corporate headquarters are located at One Kendall Square, Building 700, Cambridge, MA 02139, and its telephone number is (617) 264-1800. For more information, please visit .

Certain statements made in this press release that are not based on historical information are forward-looking statements which are made pursuant to the safe harbor provisions of the Private Securities Litigation Reform Act of 1995. This press release contains express or implied forward-looking statements relating to, among other things, management's expectations of financial performance, expectations regarding the prospective value of the commercial, system performance and technical and scientific achievements and goals discussed in this press release, estimates of expenses and future revenues and profitability, product development and marketing plans, and management's plans, objectives and strategies. These statements are neither promises nor guarantees, but are subject to a variety of risks and uncertainties, many of which are beyond Helicos' control, which could cause actual results to differ materially from those contemplated in these forward-looking statements. In particular, the risks and uncertainties include, among other things, our ability to sustain and scale our manufacturing capabilities and the commercialization process for the Helicos(TM) Genetic Analysis System; our history of operating losses and ability to achieve profitability; the research and development spending levels of academic, clinical and governmental research institutions and pharmaceutical, biotechnology and agriculture companies who may purchase our Helicos(TM) Genetic Analysis System; our reliance on third-party suppliers; competition; changing technology and customer requirements; our ability to operate in an emerging market; market acceptance of our technology; the length of our sales and implementation cycles; our dependence on large contracts for the sale and implementation of our Helicos(TM) Genetic Analysis System; failure of our technology and products; our ability to maintain customer relationships and contracts; ethical, legal and social concerns surrounding the use of genetic information; our ability to retain our personnel and hire additional skilled personnel; our ability to manage our growth while operating with limited resources; our ability to control our operating expenses; general economic and business conditions; our ability to obtain capital when desired on favorable terms; and the volatility of the market price of our common stock. Existing and prospective investors are cautioned not to place undue reliance on these forward-looking statements, which speak only as of the date hereof. Helicos undertakes no obligation to update or revise the information contained in this press release, whether as a result of new information, future events or circumstances or otherwise. For additional disclosure regarding these and other risks faced by Helicos, see the disclosure contained in Helicos' public filings with the Securities and Exchange Commission.