Posts in category JCVI

June Grant Update

Congratulations to our JCVI Principal Investigators for the several successful grants that were awarded or that we received notification of in the month of June. All of the following PIs received official confirmation of awards to be made to them. Christopher Dupont, John Glass, Granger Sutton, Daniel Gibson, Charles Merryman, Rembert Pieper, Richard Scheuermann, Christopher Town, Reed Shabman, Orianna Bretschger, Sanjay Vashee and Sarah Highlander to the sum of $6,365,099. The topics of these awards ranged from synthetic approaches to studying the human microbiome, vaccine development, protein modeling, studies on tuberculosis strain diversity, and immune profiling.

Of notable mention are the awards to be made to Sanjay Vashee $1,879,282 from the NSF (BREAD supplement that will allow for an extension of the current program focused on developing a synthetic vaccine for Bovine pleuropneumonia), Reed Shabman from DHS ($1,135,654; The development and validation of sequence subtraction databases to improve virus discovery through next generation sequencing – special acknowledgement to Tim Stockwell and Derek Harkins for their contributions to this proposal), and to Chris Town from NSF ($883,704; Federated Plant Data Base Initiative for Legumes).

A sincere Congratulations to the team.

Q&A with Jessie J. Knight, Jr.

The JCVI CEO Council is a small group of distinguished men and women who are thought leaders in business, medicine, law, the arts and humanities, and community affairs. JCVI is fortunate to have individuals willing to serve as knowledgeable and enthusiastic ambassadors for our scientists and their research, and we are excited to introduce you to our inaugural member, Jessie J. Knight, Jr., Executive Vice President for External Relations at Sempra Energy. Knight is a board member of the Seattle-based Alaska Air Group and Alaska Airline, life member of the Council on Foreign Relations in New York and member of the corporate council of the Hoover Institution of Stanford University. Knight is a well-respected businessman and philanthropist in San Diego. He is also a frustrated musician and has been playing jazz guitar for 30 years. For the past 5 years Knight has been playing the Chinese instrument called Erhu. The entire JCVI team is thrilled to have access to all of Knight’s talents and resources.

Jessie J. Knight, Jr.

Jessie J. Knight, Jr.

You are a native of Missouri. How did you end up in San Diego?

I moved to San Diego in 1999 from San Francisco after serving for six (6) years as the commissioner for the California Public Utilities Commission (CPUC), after being appointed by then-Gov. Pete Wilson. I was recruited to be the president and chief executive officer of the San Diego Regional Chamber of Commerce.

You and your wife, Joye Blount, are respected philanthropists in San Diego. How important is giving back to your community?

As the executive vice president of external affairs for Sempra Energy and with Joye being a Wealth Advisor at US Bank of the Private Client Reserve, we have a professional duty to be present and active in the community and it serves our personal philanthropic interests as well. We have a special interest for organizations that cater to military families, education, improving health and the support of women.

How did you become interested in the J. Craig Venter Institute?

Joye and I have a special interest in JCVI as we have been following the impact of the discovery of the human genome. We believe it’s not only going to have an economic impact in San Diego but also on health worldwide. We believe gaining a better understanding of genetic diseases will allow for improved health and the opportunity to change the course of medicine.

We are excited to have you join the JCVI CEO Council. What do you hope to accomplish in this new role?

Joye and I have had the opportunity to build many great relationships with many individuals and organizations. We’d like to expose JCVI to those we know and increase the reach of JCVI and drive community involvement and philanthropic support to the great work of JCVI.

What environmental/health goals do you personally hope to see JCVI tackle?

I have a personal interest in learning more about the possibilities for gene therapy. My family has been dealing with a genetic disorder for many years, and I’m hoping with my involvement with JCVI that I can understand the opportunities that genomics has for new possible treatments for rare genetic disorders.

Dr. Venter Delivers UCSD 2015 School of Medicine Commencement

Continue reading ‘Dr. Venter Delivers UCSD 2015 School of Medicine Commencement’

Johns Hopkins Announces Inaugural Recipient of Hamilton Smith Award for Innovative Research

JCVI’s Hamilton O. Smith, MD has been recognized by Johns Hopkins University with a research award in his honor. The inaugural recipient of the award is Jie Xiao, an associate professor of biophysics and biophysical chemistry at the Johns Hopkins University School of Medicine. Dr. Smith was awarded the Nobel Prize in 1978 for his discovery of restriction enzymes, work he conducted while he was a young faculty member at Johns Hopkins.

Meet Richard Scheuermann, Ph.D., JCVI’s Director of Bioinformatics

Richard H. Scheuermann, Ph.D., who joined JCVI in 2012 from the University of Texas Southwestern as the Director of Bioinformatics, is an accomplished researcher and educator. He and his team apply their deep knowledge in molecular immunology and infectious disease to develop novel computational data mining methods and knowledge representation approaches.

Richard Scheuermann

Richard Scheuermann, Ph.D., JCVI’s Director of Bioinformatics

From an early age, Richard was very interested in science and the living world around him.  He was a curious child who loved to explore the ponds and fields in his hometown of Warwick, New York.   This rural community in upstate New York is covered with dairy farms and apple orchards.  He demonstrated an early aptitude for math and science and was fortunate to have talented high school teachers who recognized his potential.   Although neither of Richard’s parents were college educated, they encouraged his academic pursuits.  When Richard and his father met the high school guidance counselor, Richard told of his intention to attend the Massachusetts Institute of Technology (MIT).  The response from the counselor was a resounding, “There is no way you’ll ever get in.” Richard applied to MIT (and only MIT) anyway, and was accepted by early decision.

At MIT Richard intended to pursue a career in chemical engineering (CE) but to his surprise, he found that he loathed the CE classes.  While trying to identify a new study path, Richard took a biochemistry class to fulfill a CE requirement.  This class would change Richard’s career path.  While at MIT, Richard worked in the lab of Annamaria Torrianni-Gorini, Ph.D. and received first hand experience in conducting scientific research.  He was inspired by his peers and professors and had found his calling. During this time he also had the privilege to study with Salvador Luria, Ph.D., David Baltimore, Ph.D., David Botstein, Ph.D., and Phil Sharp, Ph.D., all luminaries in their fields. Richard received a B.S. in Life Sciences from MIT in 1981.

Richard went on to complete his Ph.D. in Molecular Biology at the University of California, Berkeley.  After completing his doctoral research on bacterial replication fidelity at U.C. Berkeley with Hatch Echols, Ph.D., Richard was offered his own research lab in Europe.  He accepted an independent research position at the Basel Institute for Immunology in Switzerland, where he identified the CDP protein as a critical regulator of immunoglobin gene expression and the role of nuclear matrix attachment in transcription regulation.

Although Richard had trained as a molecular biologist, in 1992 he was recruited into the Department of Pathology at the University of Texas Southwestern Medical Center (U.T. Southwestern) in Dallas.  Apprehensive at the beginning to find himself in a clinical department, as he had at every previous crossroads, Richard quickly embraced the opportunity before him.  He changed his research focus to disease and disease pathogenesis, and he rose to the rank of Professor with tenure. Richard established a robust research program at U.T. Southwestern investigating signal transduction pathways that regulate normal lymphocyte development and function and that induce cell cycle arrest, apoptosis and dormancy in lymphomas. This important work was supported through numerous research grants from the National Institutes of Health, the American Cancer Society, the Texas Higher Education Coordinating Board, and other granting agencies.  In the Pathology Department, he also worked on the development and validation of novel diagnostic methods for viruses that mediate chronic infectious disease and for chromosomal translocations that drive leukemia and lymphoma development.

Half way through his U.T. Southwestern career, Richard had found life in the wet lab less and less fulfilling.  Through his involvement in several high-throughput research projects Richard realized that it was becoming relatively easy to generate lots of data but more difficult to analyze the information.  And so he decided to take a sabbatical year at the San Diego Supercomputer Center to immerse himself into the emerging field of bioinformatics. After his time in San Diego, Richard was drawn into the bioinformatics discipline, and he redirected his career with three research and development proposals funded in rapid succession.

Richard established a very successful bioinformatics program at U.T. Southwestern; however, he was searching for new opportunities to expand on his success.  In 2012, the invitation to join JCVI, a “bleeding-edge research institution that valued informatics” could not be ignored.

As the Director of Bioinformatics at JCVI, Richard leads a multi-disciplinary team of computational biologists. Richard and his team continue to develop novel computational methods to accelerate data mining and statistical analysis. These methods have been made available to the research community through several public database and analysis resources, including the Influenza Research Database (IRD;, the Virus Pathogen Resource (ViPR; and the Immunology Database and Analysis Portal (ImmPort; supported by the National Institutes of Health. His current research is focused on human pathogenic viruses—how they spread and cause disease.  He is a part of the elite community that responds to virus outbreaks, such as the recent Ebola and Enterovirus D68 occurrences.  This “real time sorting out” of emerging infectious diseases keeps his still curious New York state of mind engaged and excited about his work.

In his spare time Richard enjoys swimming, soccer and skiing and spending time with his wife, Nancy, and sons, Alex and Derek.  Over the past thirteen years, he has studied martial arts, earning his first-degree black belt.   As it was in the outskirts of Warwick, Richard continues to explore his new San Diego environment, and is rapidly becoming an avid sailor.

Richard’s commitment and determination to a path, whether on the high seas or in the lab, are unrivaled.  Like him, his peers at JCVI are excited to see where his research will take us next.

In Memory of Dr. J. Robert Beyster

The JCVI family mourns the loss of a true friend and generous supporter, Dr. J. Robert Beyster.  Dr. Beyster was a World War II Veteran, a nuclear engineer whose research propelled the Department of Defense’s weapons systems and submarines into the future of war fighting, but most notably, he founded Science Applications International Corporation (SAIC), an employee-owned multi-billion dollar corporation.

Bob and Betty Beyster

Bob and Betty Beyster

The Beyster Family have been generous supporters of science programs at the JCVI since 2009 when they, along with matching funds from Life Technologies Foundation, sponsored a two year leg of the Sorcerer II Global Ocean Sampling Expedition. This substantial support from the Beyster Family enabled sampling research of microbial life in the waters of the Baltic, Mediterranean, and Black Seas. These are scientifically important because they are among the world’s largest seas isolated from the major oceans. To date more than 80 million new genes and protein families have been discovered as part of the Sorcerer II Expedition.

The Beysters have also supported JCVI scientist Andy Allen, Ph.D. and his Southern California Upwelling Sampling Project. Dr. Allen has conducted sampling expeditions along the Southern California coast to better understand the microbes living in these waters. Dr. Beyster participated in 8 of the 11 sampling excursions that were conducted from his own boat, Solutions. He blogged about a major regional dinoflagellate bloom that was sampled as part of this project.

Importantly, this work has led to an exciting new San Diego-based collaboration between JCVI, NOAA and the Scripps Institution of Oceanography (SIO) to integrate genome-enabled techniques and technologies (i.e., ‘omics) into the California Cooperative Oceanic Fisherines Investigations (CalCOFI).  CalCOFI is a multi-partner, long-term ecosystem and fisheries study off the coast of California in it’s 7th decade.

The most recent $2.5 Million gift in 2012 for the completion of the new J. Craig Venter Institute sustainable laboratory was recognized by naming the third floor ocean view conference room and terrace the “Bob and Betty Beyster Conference Room” and the “Bob and Betty Beyster Terrace”.

Beyster Conference Room and Terrace

Left: Looking up at the Beyster Conference Room and Terrace from the ground floor. Right: Sunset on the Beyster Terrace.

Dr. Beyster will be greatly missed by his family, friends and colleagues.  We are fortunate to have a constant a reminder of his generosity and support.  A link to his obituary can be found here.

Warm Wishes

It has been another year and with that more fungus in my life (and another more human bundle of joy). I tried my best to get these fungus to behave (and my children) but we can’t always control them. So below is my newest artwork. It says Warm Wishes and is as cozy and warm (and fuzzy) of a cabin I could get with fungus. Enjoy and happy holidays to you.

Warm Wishes

Snow and smoke: Neosartorya fischeri 181; Wreath and ‘Warm wishes’: Aspergillus nidulans A4; Cabin: Aspergillus terreus 20843. Image: Stephanie Mounaud / JCVI

Inoculating loops roasting in an open fire
The negative 80 nipping at your fingers
The incubators beeping like a choir
And the aroma of bacteria just seems to linger

Everybody knows resistance and recombination
Help to give us such a fright
Teeny Tiny Bacteria with their constant mutations
Will make it hard for us to sleep at night

But they all know that scientists will find a way
We’re using sequencing and synthetic life
And every single strand of DNA
To see if we can really end the lifelong strife

And so really think before you join the craze,
You will be in the lab every day.
Although it’s rewarding, many times we’re in a daze
But we do take a break for the happy holidays!

Guest Speakers Marlo Gottfurcht Longstreet and Dean Ornish Inspire Guests at JCVI‘s “Life at the Speed of Light” Gala

On October 18, J. Craig Venter Institute (JCVI) hosted our “Life at the Speed of Light” black tie gala featuring special guests Dean Ornish, MD, and Marlo Gottfurcht Longstreet. JCVI welcomed 200 community leaders, sponsors and supporters including Representative Scott Peters, Susan Taylor, Reena Horowitz, Linda Chester, Jack McGrory, Jessie Knight, Jr., Joye Blount, Wendy Walker, Randy Woods, Andrew and Erna Viterbi, Mary Ann Beyster, and JCVI Board Member Bill Walton and wife Lori.

Guests experienced our science first hand through various displays and had the opportunity to interact with many JCVI scientists to learn how advances in genomics are impacting our health and environment.

microbiome station

JCVI Scientists Manny Torralba and Stephanie Mounaud welcomed guests with a brief introduction to the palm microbiome by taking swabs and sharing aggregate population results midevening.

Following welcome remarks by J. Craig Venter, Ph.D., Founder & CEO of JCVI, Marlo Gottfurcht Longstreet shared her son Tanner’s battle with a Giloblastoma Brain Tumor. It is understood that the tumor developed as a result of a mutation in the TP53 tumor suppressor gene. Sadly, Tanner Jay Longstreet passed away in 2013 at the age of 11.

Marlo Gottfurcht Longstreet sharing her personal story about her son Tanner and ongoing work at the Tanner Project.

Marlo Gottfurcht Longstreet sharing her personal story about her son Tanner and ongoing work at the Tanner Project.

Personal tragedy turned mission for Marlo as she set out to do everything she could to better understand what afflicted Tanner, which gave rise to the Tanner Project at JCVI. Led by Nicholas Schork, Ph.D., the Tanner Project is what is referred to as an “N of 1” project – a single patient case study. Rather than go in for yearly checkups, the patient in the study is monitored daily so that any evidence of cancer can be detected at onset. The goal is to keep the study patient at what is referred to as stage 0. By closely monitoring the condition in this “N of 1” study, its application can be applied more broadly in personalized medicine – “N of 1 for everyone.”

Dr. Ornish discussed advances in personalized medicine and how simple behavioral changes can greatly affect patient outcomes. He addressed ideas presented in his most recent book, The Spectrum, suggesting diet and exercise are not all or nothing propositions. If today wasn’t a great food day, there is no reason tomorrow can’t be. This kind of thinking can greatly improve longevity and quality of life.

Dean Ornish speaking to gala attendees on advances in medicine.

Nobel Laureate Hamilton Smith (right) walks gala attendees through JCVI advances.

Rangers and the Re-Arrangers

The evening was rounded out with a delectable dinner, dancing, and gypsy jazz music by Seattle’s Rangers and the Re-Arrangers.

JCVI is grateful to its event sponsors – CapitalOne Bank, BioMed Realty, Synthetic Genomics, Inc., Human Longevity, Inc., Thermo Fisher Scientific, Gunderson Dettmer, ZGF, and Egon Zehnder – for their support. Thank you as well to our DNA gift bag sponsors: Way Better Snacks, GoodBelly, Kowalski Communications, La Jolla Playhouse, Lean & Green Café, and Travel Set Go.

JCVI remains committed to tackling today’s pressing medical and environmental concerns, and we continue to rely on your generosity to achieve our goals. For more information on funding needs and opportunities, please contact Katie Collins as

H3Africa Update

The National Institutes of Health (NIH) and the UK-based Wellcome Trust, in partnership with the African Society of Human Genetics, developed a program to foster genomic and epidemiological research in African scientific institutions. The laboratory and computational infrastructure available to most scientists on the African continent is currently insufficient to keep up with the rapid developments in DNA sequencing technologies and the need to use advanced computationally intensive methods to analyze this data.

Through the H3Africa Consortium, a partnership between NIH and Wellcome Trust, funding has become available to support knowledge development and implementation of genomics-centered research in several African academic institutions. The first scientific paper to come from this effort, Enabeling the Genomic Revolution in Africa, was published in the journal Science in June 2014.

H3Africa Efforts at J. Craig Venter Institute (JCVI)

One of the main initiatives of H3Africa is to foster scientific exchange between US-based partners and their African-based consortium members. JCVI is involved in a number of such partnerships through training and research collaborations.

Tuberculosis Research with Addis Ababa University

Addis Ababa University is the only Ethiopian institution to receive a primary award from NIH under H3Africa. It is based on a collaboration with JCVI. Professor Gobena Ameni of Addis Ababa University and Dr. Rembert Pieper of JCVI developed a proposal on Systems Biology for Molecular Analysis of Tuberculosis in Ethiopia which was initiated earlier this year. The research focuses on genomic variability in M. tuberculosis strains in Ethiopian pastoralist societies and also has an oral microbiome and proteomic biomarker discovery component.

Bioinformatics Training for African Scientists

As part of H3Africa, JCVI is leveraging its recent GCID award, where appropriate, for training of African Scientists. As part of this effort Dr. Andrey Tovchigrechko  taught microbiome analysis to graduate students in Ibadan, Nigeria. The workshop was organized by the local H3Africa Bioinformatics Network node. The workshop took place in July, 2014 and comprised of students from Nigeria and other West and Central African countries.

Symposium presenters.

Symposium presenters.

Workshop student participants.

Workshop participants.

The workshop was held at IITA.

The workshop was held at IITA.

During the three day workshop, Dr. Tovchigrechko taught the students launching and controlling computing instances on Amazon cloud, the basics of Python and R programming, MG-RAST Web interface, MG-RAST R package matR and JCVI-developed R code MGSAT. MG-RAST tutorials were provided by one of its developers Andreas Wilke (ANL).

Dr. Tovchigrechko also gave a talk, along with a dozen other speakers, at a one-day symposium at the University of Ibadan that preceded the workshop and included approximately 200 participants. Special thanks go to Nash Oyekanmi, the organizer and manager of the whole event, for his relentless efforts.

Collaborations with University of Cape Town

Also as part of the H3Africa Consortium, Dr. William Nierman from JCVI and Dr. Mark Nicol from the University of Cape Town, South Africa are in collaboration to study the nasopharyngeal microbiome and respiratory disease in African children. Dr. Nierman’s group has conducted a month long in house microbiome training workshop with students from Dr. Nicol’s group.

The focus of the training was to teach students JCVI’s complete microbiome pipeline (including sample preparation, sequencing generation, and final association analysis). The aim of the training collaboration is to ensure that this complete pipeline can be performed at the University of Cape Town, to help build independent and sustainable capacity in this field within South Africa.


J. Craig Venter at Recent Google Zeitgeist Conference [VIDEO]

Dr. J. Craig Venter recently spoke at a Google Zeitgeist conference in Arizona where he spoke on advances in genomics, synthetic biology, and DNA as the software of life.