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These articles were published in U.S. 1 Newspaper on June 2, 1999.
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Life in the Fast Lane: Compugen
Scientists on the cusp of this century who are trying
to develop therapies from genomic and protein sequences can be likened
to the gold miners of the 19th century. They each must sift through
the mud and water for countless hours before finding the gold. For
the ’49ers, it was nuggets of metal; for scientists it is useful sequences
of DNA and proteins.
But unlike the miners, today’s gold diggers have the tool of bioinformatics
to help them shovel, sift, and determine what’s gold.
One company with a high-tech sieve is Israel’s Compugen, which has
recently moved into the Exit 8A area to set up a secondary research
and development home. Compugen’s use of bioinformatics is the sieve
with the ability to analyze gene sequences thousands-folds faster
than through traditional laboratory screening and other analysis methods
"Bioinformatics is the application of computer technology in order
to model and understand the molecular mechanisms of life," says
Simchon Faigler, one of the founders of Compugen and the vice president
of technology. He sees Compugen’s place in the pharmaceutical field
as using bioinformatics to convert the ever-increasing pool of genetic
data from raw material into meaningful information. The ultimate goal
is to pave the way for cures and therapies.
"Our customers are looking for genes that have some effect on
specific pathologies or diseases," says Faigler. The key to Compugen’s
speed is algorithms, or mathematical formulas, that dictate how the
computer hunts for similarities between sequences and how it identifies
a match. "Sequences are small pieces of a very large puzzle,"
says Faigler. "Our program tries to assemble them together to
build up a bigger picture."
The algorithms Compugen has embedded in its products increase the
speed at which meaningful information can be extracted from genomic
and protein sequence data, accelerating the discovery of new drug
targets. By using its own technology, Compugen researchers have been
able to identify over 3,000 genes that were previously unknown. They
used standard experimental methods to estimate that more than 90 percent
of these new gene forms (more than 2,700 genes) are real — they
are in present in human cells.
The company has reached significant milestones in its short history.
Last year Compugen won a contract from the U.S. Patent and Trademark
Office to supply software and hardware for examining biological patent
applications and accelerating the approval process. Compugen’s products
will analyze the extensive protein and DNA sequence data being submitted
in the patent applications.
Another coup happened last October, when the company signed a three
year, multimillion dollar collaboration with Parke-Davis for the LEADS
drug target discovery platform. This platform addresses two problems
facing researchers today. "It takes all known data and clusters
this data together, solving the puzzle of how to build genes out of
the fractional data available right now," says Faigler. "Then,
out of these genes that we built, we can fish out those that might
be useful to the life science or the pharmaceutical researchers."
Compugen has also finished its fourth round of financing. "Each
round was bigger," says Faigler. Far from the seed capital of
$100,000 per year Compugen received in 1993, the end of 1998 saw the
close of a $15 million equity private placement. Clal Biotechnologies
Industries, one of Israel’s investment firms, led the financing. Other
financiers of this round include Hapoalim Investments, Ampal, Evergreen
Funds, and Cayrex Private Equity.
When the company began, its one financial supporter was the Israeli
government, which granted seed money and a place to work — in
the Negev desert town of Sde-Boker. The company recently moved to
the metropolitan Tel Aviv. And despite the office in New Jersey, Compugen
has no plans to sell itself off to American bidders like some Israeli
companies are doing. "I don’t think we’ll even consider it,"
All the money made by the company is being invested back into research
and development. It has not recorded any profits in six years, and
a rough estimate by Faigler predicts five more profitless years.
Compugen and the field of bioinformatics have grown with the expectation
that new drugs and therapies will be derived from information gleaned
from the blueprint of the human genome. With only a fraction of the
100,000 human genes already discovered, the database of information
is massive and the challenge is picking out the useful information
from the junk.
The company’s first product — the Bioaccelerator — was a piece
of specialized hardware that attached to a workstation and could accelerate
certain analysis software by three orders of magnitude. Since then
the company has developed the BioXL which is even faster than the
Customers came soon after the products were offered. Merck bought
the first Compugen machine (slightly larger than a personal computer)
in 1994 and has since bought two more, at about $200,000 each.
In 1995 the company began to market GenCore software, the first sequence
analysis package designed for high throughput environments — where
thousands of genes and other biological sequences are analyzed daily.
The software, packaged with the company accelerators, has become the
de facto standard for high throughput sequence analysis, says Faigler.
Compugen is selling the acceleration hardware and software products
to an impressive array of big pharmas and smaller firms. In addition
to Parke Davis and Merck, the clients include SmithKline Beecham,
Amgen, Eli Lilly, Bayer, Wyeth Ayerst, Human Genome Sciences, Incyte
Pharmaceuticals, and Millennium Pharmaceuticals. Collaborators include
Parke-Davis, EBI (in the United Kingdom), the Sanger Centre (UK),
and the Weizmann Institute in Israel.
As far as competition goes, no one comes close to providing what Compugen
does, says Faigler. But to evaluate his claim one must step back to
look at the contenders in the various contests:
is battling it out with entrepreneur Craig Venter of P.E. Celera to
try to sequence the complete human DNA located in the 23 chromosomes.
Scientists believe there are between 100,000 and 150,000 human genes
embedded within those chromosomes.
"They are trying to measure the sequences at the DNA level, the
home of the chromosomes, trying to extract the DNA code from the 23
pairs of chromosomes present in every human cell," says Faigler.
"After they finish doing it all the raw data of the human genome
will be known." The government-funded method has the reputation
of being more accurate but significantly slower. Scientists claim
Venter’s method is risky, but if he succeeds he will have the data
before it enters the public domain.
Rockville, Maryland, and NIH’s National Center for Biotechnology Information
have built gene databases out of available data. The NIH database
is called Unigene.
A quick tutorial: DNA (in the nucleus of the cell) is the template
that generates the RNA. The RNAs, in turn, are translated into mature
RNAs (MRNAs) which in turn are translated into proteins, which do
the actual work. Random short samples of MRNA (very close to the proteins
themselves) are called ESTs or expressed sequence tags. These ESTs
are the most popular subject for current research.
Faigler says that TIGR and NCBI are using only the ESTs for their
input data. In contrast, Compugen works with almost all of the available
public data: ESTs, MRNAs, and the actual DNA. "We are taking all
the known data including the genomic data from the HGP project and
analyzing it together," says Faigler.
Compugen’s analysis is superior, Faigler says, "because the quality
and level of pharmaceutically relevant information that you can extract
from this data is higher than the raw data itself." He also says
Compugen has better modeling of the biological processes that generate
the data. "We can reverse-build the pieces of the puzzle and get
more accurate results."
"We build genes out of this data," says Faigler, "and
genes and the function of genes are what people are looking for."
Sometimes fate brings people together and sometimes
it’s mandated military service. The latter was the case for the three
founders of Compugen, who formed their company in 1993 after each
had finished serving for the Israeli army. Eli Mintz, Amir Natan,
and Simchon Faigler took their studies of math, science and computers
into the field of bioinformatics.
Mintz, the CEO and president, developed algorithms and wrote and managed
software for Israel Aircraft Industries’ Mabat subsidiary. Natan,
VP of software, developed algorithms and signal processing software
at Rafael, the National Armaments Development Authority. Both are
still in Israel.
Simchon Faigler moved to the U.S. in September. Faigler, along with
the others, studied at the Hebrew University where he earned a BA
in physics and mathematics. He spent the rest of his time there in
the communications division, in development of rapid hardware for
smart communication systems. After a year as an independent consultant
for the defense industry, he joined his army colleagues to start a
company outside the area of defense. He currently lives in Edison
with his wife, Ruth, an accountant, and their son and daughter.
The Israeli company is closing its first U.S. branch, in Woburn, just
outside Boston. Sales and customer support staff from that office
will move to Exit 8A, along with new hires and employees from Russia
and Israel. In two months the Exit 8A office will have 13 employers;
it will expand its R&D efforts and continue to support partners and
customers in the area. Compugen has grown to nearly 100 employees
"Our object in the future is to concentrate on big customers —
the 50 large pharmaceuticals," says Faigler. "New Jersey is
a very good place to be."
— Monika J. Guendner
Simchon Faigler, VP, technology. 609-655-5105; fax, 609-655-5114.
Home page: http://www.cgen.com.
Enough discussion, the Department of Transportation
is saying, about the Millstone Bypass. With or without the support
of Princeton Township and Borough, we’re going to build it. "After
working close to 20 years on this project we need to move forward.
Further analysis would not help the motorists on Route 1," says
DOT spokesman John Dourgarian, after a meeting last week on the $50
million project. "There is rarely a transportation project that
has unanimous support, but it was very clear that West Windsor, the
Princeton Chamber, Mercer County, Princeton University, Eden Institute,
and Sarnoff are all in strong support."
"Based on the fact that the project is entirely in West
Windsor, we should advance this project as fast we possibly can,"
The process: a public information session this summer, environmental
assessment by fall, a public hearing in the fall, environmental review
by the Federal Highway Administration, final design, and property
acquisition. "We feel we can start construction in 2002 and complete
it in two years."
What will happen: A cloverleaf will be built at Route 1 and Harrison,
eliminating the traffic signals at Harrison and Washington and Fisher
Place. Eden will move nearby to new quarters built and funded by Princeton
University. The bypass road will start at the railroad bridge in Princeton
Junction, proceed through Sarnoff property and over the cloverleaf.
Motorists can either peel off at Harrison or continue along the canal
to turn right on Washington Road.
Opponents of the original plan can claim minor victories: The opportunity
to enter and leave Princeton under the archway of Washington Road’s
dramatic elms will be preserved, because Washington Road will remain
open for right turns on and off Route 1.
The bypass road was downgraded from 45 or 50 miles per hour to 40
miles per hour and will be posted at 35. Instead of coming within
350 feet from the Delaware & Raritan Canal, the closest point now
is 500 feet. A signal will disperse traffic at the point where the
bypass road intersects Washington Road.
What won’t happen: The Washington Road circle will not be replaced
by an underpass, nor will the bypass be extended from Washington Road
to Alexander Street.
— Barbara Fox
3206 Route 206 and Orchard Road, Box 183, Princeton 08542-0183. John
Short, chairman and CEO. 908-281-5100; fax, 908-281-5105.
The company announced the acquisition of Macro International
Corp., another market research firm, for $28 million on Friday, May
28. This will nearly double the size of the 61 year-old firm, and
place it among the top 10 market research companies in the US. While
most Opinion Research clients are Fortune 500 corporations, most of
Macro’s business comes from government contracts. The acquisition
will mean Opinion Research will have offices in Europe, Latin America,
Asia and Africa, as well as the US.
The expansion comes on the heels of former CEO Michael Cooper’s resignation
in February. John F. Short, former chief financial officer, is now
both chairman and CEO.
Suite 212, Princeton 08540. William J. Healy, president. 609-924-2882;
fax, 609-924-5090. Home page: http://www.fsu.org.
Yipinet, a California-based Internet company, has bought
Princeton Learning Systems, and the two companies will merger their
online learning systems. Princeton Learning Systems was founded four
years ago (U.S. 1, November 25, 1998, and March 24, 1999) to design,
implement, and manage Internet and Intranet-based systems for training,
testing and regulatory compliance. Its core software product providing
access testing and reporting via the web, and its chief virtual product
is Financial Services University.
Yipinet is 18 months old, funded to the tune of $18.5 million, and
plans to go public this year. The Princeton branch of the company
will stay on State Road and retain its employees; William Healy will
stay with the new company and be president of PLS Services, and Steven
Haase will be vice president of sales and financial services.
08542-1423. Joseph A. Allegra, president. 609-497-0205; fax, 609-497-0302.
Home page: http://www.princetonsoftec.com.
Princeton Softech has bought SELECT Software Tools PLC,
which has a product line that meshes with Princeton Softech’s eData
distribution and management technologies — Object Oriented, Component-Based
Development products for developing and implementing Java and C++
Princeton Softech has bought all the assets of SELECT, which will
continue its R&D activities at its current home office in Cheltenham,
England. Princeton Softech, a subsidiary of Computer Horizons Corp.,
has 110 employees on State Road. SELECT is also a public company (Nasdaq:
Building 1, Suite 3, East Windsor 08520. Shandy Amin, CEO. 609-371-5111.
Home page: http://www.trishusa.com.
TRISH USA Corp, a developer of workflow management and customer care
software, has opened an office on Princeton-Hightstown Road. The 10-year
old company moved from the Secaucus area. TRISH also has an office
in Brazil, where the majority of its clients are located.
The six-person staff on Princeton-Hightstown Road develops and customizes
software for clients including Lucent and Embertel.
Building 3, East Windsor 08520. Ragu Patel, managing director. 609-426-9002;
The Alpha Group, a boutique investment banking firm that specializes
in financial transactions for businesses with revenues between $100,000
and $25 million, has opened its third office at 379 Princeton-Hightstown
Road. The company also has locations in Woodbridge and Virginia.
Alpha Capital Corp., as the new branch is called, will focus on the
emerging technology sector companies, assisting them in fundraising,
business planning and preparation for IPO.
Street, Princeton 08540. Stephen Balch, president. 609-683-7878; fax,
609-683-0316. Home page: http://www.nas.org.
The National Association of Scholars, founded in 1987, was scheduled
to move its headquarters from 575 Ewing Street to 221 Witherspoon
Street on Tuesday, June 1. Phone and fax numbers are the same.
08540. William F. King III, president. 609-951-6900; fax, 609-951-6935.
The real estate development firm moved from 504 Carnegie Center.
Fridkis, founder. 609-924-6880; fax, 609-924-6890. Home page: http://www.kllabs.com.
K&L Labs, a pre-press and offset printing firm, moved from Route 571
to 33 Wall Street. Phone and fax numbers are new.
Center, Suite 204, Monmouth Junction 08852. Wlodek Mandecki, president
and CEO. 732-355-0100; fax, 732-635-0428. Home page: http://www.pharmaseq.com.
PharmaSeq Inc. has signed an agreement with Sarnoff Corporation for
Sarnoff to design and make miniature micro-transponders that will
transmit the identity of DNA sequences coded into the transponders.
It also announced a $250,000 investment by the NJ Commission on Science
and Technology to commercialize light-powered micro-transponders in
a radio-frequency identification system.
Trenton 08618. H. Joan Pennington, executive director. 609-394-1506;
The nonprofit organization providing sliding scale and pro bono legal
services has received a grant of $236,998 from the Office of Justice
Programs in the U.S. Department of Justice to expand its services
for domestic violence victims. The funds will be used to train and
appoint attorneys specializing in domestic violence in Mercer, Burlington,
and Ocean counties. Women’s Law Project (WLP) was founded in 1997,
under the aegis of the National Center for Protective Parents Inc.
Hailing the grant as an endorsement of WLP’s mission to secure quality
legal representation for domestic violence victims Pennington says,
"These women have lost their children, lost their property, and
even lost their safety by going into court unrepresented or representing
themselves." WLP’s attorneys work with the shelter in Mercer County
operated by Womanspace and the shelters in Burlington and Ocean counties
operated by Providence House.
Forrestal Village, Princeton 08540. Paul M. Lewis, executive director.
609-514-0001; fax, 609-514-0005.
Paul M. Lewis is now executive director at this retirement community
developed by CareMatrix Corporation of Needham, Massachusetts. It
includes Chancellor Park (an assisted living community), Forrestal
Skilled Nursing and Rehabilitation Center, and independent townhouses.
Lewis went to the University of Vermont.
Princeton 08540. Lew Lancaster, general secretary. 609-921-7866; fax,
Consultation on Church Union, a 30-year-old organization promoting
interdenominational unity among nine member churches, closed its office
on Wall Street Friday, May 28. Daniell Hamby, the general secretary,
is taking over the parish at St. Andrew’s Episcopal church in Yardley.
The organization is looking for a new executive. Lew Lancaster, a
resident of Louisville, Kentucky, who has been with the Christian
ministry for 40 years, will act as general secretary in the interim.
Jack Honore’s Barber Shop on Palmer Square.
established and ran the Farm School and Camp Rogapeki-J.
of the Department of Community Affairs and a professor at Rutgers.
P.J.’s Pancake House for 30 years.
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