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A rendering of Beelzebufo, a mammoth-sized ancient frog discovered in 2008 by David Krause of Stony Brook University, by Luci Betti-Nash
Luci Betti-Nash drawing warblers
A rendering of Rahonavis, a bird-like feathered dinosaur discovered in Madagascar
Trans Saharan Seaway
Vintana sertichi reconstruction

By Daniel Dunaief

It started over four decades ago, with a “help wanted” advertisement.

Luci Betti-Nash needed money for art supplies. She answered an ad from the Stony Brook University Department of Anatomical Sciences that sought artists who could draw bones. She found the work interesting and realized that she could “do it fairly easily. I could not have imagined a more fulfilling career.”

Betti-Nash spent 41 years responding to requests to provide illustrations for a wide range of scientific papers, contributing images that became a part of charts and graphs and drawing everything from single-celled organisms to dinosaurs. She retired last April.

Her coworkers at Stony Brook, many of whom collaborated with her for decades, appreciated her contributions and her passion and precision for her job.

Maureen O’Leary, Professor in the Department of Anatomical Sciences, said Betti-Nash’s work enhanced her professional efforts. “I couldn’t have had the same career without her,” O’Leary wrote in an email. “Artists are true partners.”

O’Leary appreciated how Betti-Nash noticed parts of the work that scientists miss. 

“I think the most important thing is figuring out together what to put in and what to leave out of a figure,” O’Leary explained. “A photograph shows everything and it can be a blizzard of detail, really too much, and it will not focus the eye. The artist-scientist collaboration is about simplifying the detail to show what is important and how to show it clearly.”

One of O’Leary’s favorite illustrations from Betti-Nash was a pull-out, color figure that envisioned the ancient Trans-Saharan Seaway from about 75 million years ago. The shallow sea, which was described in the movie “Aquaman,” supported numerous species that are currently extinct. Betti-Nash created a figure that showed these creatures in the sea and how water drained from nearby mountains, all superimposed over the geology.

“It told the story of how ancient life turned into rocks and fossils,” O’Leary explained.

Betti-Nash, who continues to sketch from her home office and plans to be selective about taking on future assignments, has numerous stories to tell about her work.

For starters, the world of science is rife with jargon. When she was starting out, she didn’t always stop researchers who tossed around the terms that populate their life as if they were a part of everyone’s vocabulary.

“Some [scientists] would come in and assume you knew exactly what they were talking about,” Betti-Nash said. “It was something they were studying for years. They would assume you knew all the terminology.”

Each discipline, from cell biology to gross anatomy to dinosaur taxonomy had its own terminology, some of which “was way over my head,” she said. 

Early in her career, Betti-Nash felt she didn’t know details she thought she should.

“The older I got, the bolder I got about asking” scientists to explain what they meant in terms she could understand, she said, adding that she felt fortunate to have scientists who were “more than willing and eager to answer my questions when I was bold enough to ask. That was one of the many life lessons I learned … don’t be afraid to ask questions.”

Betti-Nash sometimes had to work under intense time pressure. Collaborating with David Krause, who was at Stony Brook and is now Senior Curator of Vertebrate Paleontology in the Department of Earth Sciences at the Denver Museum of Science, Betti-Nash illustrated the largest frog ever discovered, which lived in Madagascar over 65 million years ago. Called the Beelzebufo, this frog weighed in at a hefty 10 pounds and was 16 inches. Ribbit!

A short time before going to press, the scientific team decided they needed a common object as a frame of reference to compare the size of this ancient amphibian and the largest living frog in Madagascar.

“We scrambled,” Betti-Nash recalled. “We decided on a pencil.” 

She didn’t have time to draw the pencil, so she put it on her scanner, did some quick painting in Photoshop, put a shadow in, added it to the scan of the painting, saved it in the format required for the journal and sent it off.

“Adding the pencil was one of those typical strokes of genius that [Betti-Nash] routinely added to artwork,” explained Krause in an email. “Everyone knows the size of a number 2 pencil.”

Even though she hadn’t sculpted in 32 years, she had to create a sculpture of the frog that students could touch. The sculpture had to be non-toxic, dry and ready within three days.

Betti-Nash turned to the Guild of Natural Science Illustrators, asking for help with ideas for the materials. She also asked Joseph Groenke from Krause’s lab to contribute his fossil preparing experience. She used an epoxy clay that she massaged into shape, and then colored it with acrylic, non-toxic paints.

That sculpture was featured as a part of a display at Stony Brook Hospital for years and has since traveled with Krause to Denver where “kids especially love it, in part because it is touchable,” Krause wrote.

Krause was grateful for a partnership with Betti-Nash that spanned almost 40 years.

“There is no doubt in my mind that [Betti-Nash] made me a better scientist and there is also no doubt that my science is better” because of her, he explained. Krause described her stipple drawings as “incredibly painstaking to execute.” His favorite is of a large fossil crocodile found in Madagascar from the Late Cretaceous called Mahajangasuchus. 

Betti-Nash urges artists considering entering the field of scientific illustrating to attend graduate school or even to take undergraduate courses, which would provide time to learn skills and terminology before working in the field.

She also suggests artists remain “interested in what you’re drawing at that moment, no matter what it is,” she said, adding that drawing skills provide a solid foundation for a career in science illustrating. Computer skills, which help with animation and videos, are good tools to learn as well.

Growing up in Eastchester, Betti-Nash often found herself doodling patterns in her notebooks. When she worked on graph paper, she colored in the squares. She also received artistic guidance from her father, the late John Betti.

A graphic designer, Betti worked for a company in Westchester, where he designed the town seal for Tuckahoe as well as the small airplane wings children used to get when they flew on planes.

During World War II, Betti, who grew up in Corona, Queens, used his artistic skills to create three-dimensional models from aerial photographs. Stationed close to the residence of his extended family in Italy during part of the war, Betti also created watercolor paintings of the Italian landscape.

When she was growing up, Betti-Nash had the “best model-making teacher in my dad,” who taught her to create paper maché.

Married to fellow illustrator Stephen Nash, Betti-Nash plans to remain active as an artist, doing her own illustrations involving nature and the relationship between birds and the environment. 

She currently leads Second Saturday Bird Walks at Avalon Nature Preserve in Stony Brook and Frank Melville Memorial Park in Setauket through the Four Harbors Audubon Society (4HAS.org)

Betti-Nash is pleased with a career that all started with a response to an ad in the paper. “I feel very privileged to have had the opportunity to work as a scientific illustrator,” she said. “I hope I was able to help communicate the science behind the discoveries that the amazing scientists at Stony Brook made during my time there.”

All photos courtesy of Luci Betti-Nash

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From left, Research Assistant Onur Eskiocak, CSHL Fellow Semir Beyaz and graduate student Ilgin Ergin. Photo by Gina Motisi, 2019/CSHL.

By Daniel Dunaief

It’s a catch-22: some promising scientific projects can’t get national funding without enough data, but the projects can’t get data without funding.

That’s where private efforts like The Mark Foundation for Cancer Research come in, providing coveted funding for promising high-risk, high-reward ideas. Founded and funded by Pamplona Capital Management CEO Alex Knaster in 2017, the Foundation has provided over $117 million in grants for various cancer research efforts.

Tobias Janowitz

This year, The Mark Foundation, which was named after Knaster’s father Mark who died in 2014 after contracting kidney cancer, has provided inaugural multi-million dollar grants through the Endeavor Awards, which were granted to three institutions that bring scientists with different backgrounds together to address questions in cancer research. 

In addition to teams from the University of California at San Francisco and a multi-lab effort from Columbia University, Memorial Sloan Kettering Cancer Center and Johns Hopkins University School of Medicine, Cold Spring Harbor Laboratory scientists Tobias Janowitz and Semir Beyaz received this award.

“We are absolutely delighted,” Janowitz wrote in an email. “It is a great honor and we are excited about the work.” He also indicated that the tandem has started the first set of experiments, which have produced “interesting results.”

The award provides $2.5 million for three years and, according to Janowitz, the researchers would use the funds to hire staff and to pay for their experimental work.

Having earned an MD and a PhD, Janowitz takes a whole body approach to cancer. He would like to address how the body’s response to a tumor can be used to improve treatment for patients. He explores such issues as how tumors interact with the biology of the host.

Semir Beyaz

Semir Beyaz, who explores how environmental factors like nutrients affect gene expression, metabolic programs and immune responses to cancer, was grateful for the support of the Mark Foundation.

Beyaz initially spoke with the foundation about potential funding several months before Janowitz arrived at Cold Spring Harbor Laboratory. When the researchers, whose labs are next door to each other, teamed up, they put together a multi-disciplinary proposal.

“If the risks [of the proposals] can be mitigated by the innovation, it may yield important resources or new paradigms that can be incorporated into research proposals that can be funded by the [National Institutes of Health] and other government agencies,” Beyaz said.

Janowitz wrote that he had a lunch together in a small group with Knaster, who highlighted the importance of “high-quality data and high-quality data analysis to advance care for patients with cancer.”

Michele Cleary, the CEO of The Mark Foundation, explained that the first year of the Endeavor program didn’t involve the typical competitive process, but, rather came from the Foundation’s knowledge of the research efforts at the award-winning institutions.

“We wanted to fund this concept of not just studying cancer at the level of the tumor or tumor cells themselves, but also studying the interaction of the host or patient and their [interactions] with cancer,” Cleary said. “We thought this was a fantastic project.”

With five people on the Scientific Advisory Committee who have PhDs at the Foundation, the group felt confident in its ability to assess the value of each scientific plan.

Scientists around the world have taken an effective reductionistic approach to cancer, exploring metabolism, neuroendocrinology and the microbiome. The appeal of the CSHL effort came from its effort to explore how having cancer changes the status of bacteria in the gut, as well as the interplay between cancer and the host that affects the course of the disease.

From left, Becky Bish, Senior Scientific Director, Ryan Schoenfeld, Chief Scientific Officer and Michele Cleary, CEO of The Mark Foundation at a workshop held at the Banbury Center at Cold Spring Harbor Laboratory in September 2019. Photo by Constance Brukin.

These are “reasonable concepts to pursue, [but] someone has to start somewhere,” Cleary said. “Getting funding to dive in, and launch into it, is hard to do if you can’t tell a story that’s based on a mountain of preliminary data.”

Beyaz said pulling together all the information from different fields requires coordinating with computational scientists at CSHL and other institutions to develop the necessary analytical frameworks and models. This includes Cold Spring Harbor Laboratory Fellow Hannah Meyer and Associate Professor Jesse Gillis.

“This is not a simple task,” Beyaz said. The researchers will “collaborate with computational scientists to engage currently available state-of-the-art tools to perform data integration and analysis and develop models [and] come up with new ways of handling this multi-dimensional data.”

Cleary is confident Janowitz and Beyaz will develop novel and unexpected insights about the science. “We’ll allow these researchers to take what they learn in the lab and go into the human system and explore it,” she said.

The researchers will start with animal models of the disease and will progress into studies of patients with cancer. The ongoing collaboration between CSHL and Northwell Health gives the scientists access to samples from patients.

With the Endeavor award, smaller teams of scientists can graduate to become Mark Foundation Centers in the future. The goal for the research the Foundation funds is to move towards the clinic. “We are trying to join some dots between seemingly distinct, but heavily interconnected, fields,” Beyaz said.

Beyaz has research experience with several cancers, including colorectal cancer, while Janowitz has studied colorectal and pancreatic cancer. The tandem will start with those cancers, but they anticipate that they will “apply similar kinds of experimental pipelines” to other cancer types, such as renal, liver and endometrial, to define the shared mechanisms of cancer and how it reprograms and takes hostage the whole body, Beyaz said. 

“It’s important to understand what are the common denominators of cancer, so you might hopefully find the Achilles Heel of that process.”

While Cleary takes personal satisfaction at seeing some of the funding go to CSHL, where she and Mark Foundation Senior Scientific Director Becky Bish conducted their graduate research, she said she and the scientific team at the foundation were passionate to support projects that investigated the science of the patient.

“No one has tried to see what is the cross-talk between the disease and the host and how does that actually play out in looking at cancer,” said Cleary, who earned her PhD from Stony Brook University. “It’s a bonus that an institution that [she has] the utmost respect for was doing something in the same space we cared” to support.

The CSHL research will contribute to an understanding of cachexia, when people with cancer lose muscle mass, weight, and their appetite. Introducing additional nutrition to people with this condition doesn’t help them gain weight or restore their appetite.

Janowitz and Beyaz will explore what happens to the body physiologically when the patient has cachexia, which can “help us understand where we can intervene before it’s too late,” Cleary said.

The CSHL scientists will also study the interaction between the tumor and the immune system. Initially, the immune system recognizes the tumor as foreign. Over time, however, the immune system becomes exhausted.

Researchers believe there might be a “tipping point” in which the immune system transitions from being active to becoming overwhelmed, Cleary said. People “don’t understand where [the tipping point] occurs, but if we can figure it out, we can figure out where to intervene.”

Scientists interested in applying for the award for next year can find information at the web site: https://themarkfoundation.org/endeavor/. Researchers can receive up to $1 million per year for three years. The Mark Foundation is currently considering launching an Endeavor call for proposals every other year.

 

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Brookhaven Lab Scientist Guobin Hu loaded the samples sent from researchers at Baylor College of Medicine into the new cryo-EM at LBMS. Photo from BNL

On January 8 the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory welcomed the first virtually visiting researchers to the Laboratory for BioMolecular Structure (LBMS), a new cryo-electron microscopy facility. DOE’s Office of Science funds operations at this new national resource, while funding for the initial construction and instrument costs was provided by NY State. This state-of-the-art research center for life sciences imaging offers researchers access to advanced cryo-electron microscopes (cryo-EM) for studying complex proteins as well as the architecture of cells and tissues.

Many modern advances in biology, medicine, and biotechnology were made possible by researchers learning how biological structures such as proteins, tissues, and cells interact with each other. But to truly reveal their function as well as the role they play in diseases, scientists need to visualize these structures at the atomic level. By creating high-resolution images of biological structure using cryo-EMs, researchers can accelerate advances in many fields including drug discovery, biofuel development, and medical treatments.

During the measurement of the samples, the LBMS team interacted with the scientists from Baylor College of Medicine through Zoom to coordinate the research. Photo from BNL

This first group of researchers from Baylor College of Medicine used the high-end instruments at LBMS to investigate the structure of solute transporters. These transporters are proteins that help with many biological functions in humans, such as absorbing nutrients in the digestive system or maintaining excitability of neurons in the nervous system. This makes them critical for drug design since they are validated drug targets and many of them also mediate drug uptake or export. By revealing their structure, the researchers gain more understanding for the functions and mechanisms of the transporters, which can improve drug design.  The Baylor College researchers gained access to the cryo-EMs at LBMS through a simple proposal process.

“Our experience at LBMS has been excellent. The facility has been very considerate in minimizing user effort in submission of the applications, scheduling of microscope time, and data collection,” said Ming Zhou, Professor in the Department of Biochemistry of Molecular Biology at Baylor College of Medicine.

All researchers from academia and industry can request free access to the LBMS instruments and collaborate with the LBMS’ expert staff.

“By allowing science-driven use of our instruments, we will meet the urgent need to advance the molecular understanding of biological processes, enabling deeper insight for bio-engineering the properties of plants and microbes or for understanding disease,” said Liguo Wang, Scientific Operations Director of the LBMS. “We are very excited to welcome our first visiting researchers for their remote experiment time. The researchers received time at our instruments through a call for general research proposals at the end of August 2020. Since September, we have been running the instruments only for COVID-19-related work and commissioning.”

LBMS has two cryo-electron microscopes—funded by $15 million from NY State’s Empire State Development—and the facility has space for additional microscopes to enhance its capabilities in the future. In recognition of NY State’s partnership on the project and to bring the spirit of New York to the center, each laboratory room is associated with a different iconic New York State landmark, including the Statue of Liberty, the Empire State Building, the Stonewall National Monument, and the Adam Clayton Powell Jr. State Office Building.

“By dedicating our different instruments to New York landmarks, we wanted to acknowledge the role the State played in this new national resource and its own unique identity within Brookhaven Lab,” said Sean McSweeney, LBMS Director. “Brookhaven Lab has a number of facilities offering scientific capabilities to researchers from both industry and academia. In our case, we purposefully built our center next to the National Synchrotron Light Source II, which also serves the life science research community. We hope that this co-location will promote interactions and synergy between scientists for exchanging ideas on improving performance of both facilities.”

Brookhaven’s National Synchrotron Light Source II (NSLS-II) is a DOE Office of Science User Facility and one of the most advanced synchrotron light sources in the world. NSLS-II enables scientists from academia and industry to tackle the most important challenges in quantum materials, energy storage and conversion, condensed matter and materials physics, chemistry, life sciences, and more by offering extremely bright light, ranging from infrared light to x-rays. The vibrant structural biology and bio-imaging community at NSLS-II offers many complementary techniques for studying a wide variety of biological samples.

“At NSLS-II, we build strong partnership with our sister facilities, and we are looking forward to working closely with our colleagues at LBMS. For our users, this partnership will offer them access to expert staff at both facilities as well as to a versatile set of complementary techniques,” said NSLS-II Director John Hill. “NSLS-II has a suite of highly automated x-ray crystallography and solution scattering beamlines as well as imaging beamlines with world-leading spatial resolution. All these beamlines offer comprehensive techniques to further our understanding of biological system. Looking to the future, we expect to combine other x-ray techniques with the cryo-EM data to provide unprecedented information on the structure and dynamics of the engines of life.”

LBMS operations are funded by the U.S. Department of Energy’s Office of Science. NSLS-II is a DOE Office of Science user facility.

Brookhaven National Laboratory is supported by the U.S. Department of Energy’s Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, visit https://energy.gov/science.

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Jeremy Borniger. Photo from CSHL

By Daniel Dunaief

Much as New Yorkers might want to minimize sleep, even during the pandemic when the need to be active and succeed is hampered by limited options, the body needs rest not only for concentration and focus, but also for the immune system.

Recently, Assistant Professor Jeremy Borniger, who joined Cold Spring Harbor Laboratory in January, collaborated with his former colleagues at Stanford University to publish research in the journal Science Advances that sheds light on the mechanism involved in this linkage.

Doctors and researchers had known for a long time that the release of glucocorticoids like cortisol, a stress hormone, can suppress the ability to fight off an infection. “That happens in people that are chronically stressed, even after surgery,” said Borniger in a recent interview.

A comprehensive understanding of the link between neuronal cells that are active during stress and a compromised immune system could help develop new ways to combat infections. The Stanford-led study provides evidence in a mouse model of the neuronal link between stress-induced insomnia and a weakened immune system.

Ideally, scientists would like to understand the neural pathways involved, which could help them design more targeted approaches for controlling the immune system using natural circuitry, according to Borniger.

Scientists could take similar approaches to the therapies involved with Parkinson’s, depression and obesity to increase or decrease the activity of the immune system in various disease states, instead of relying on a broader drug that hits other targets throughout the body.

In theory, by controlling these neurons, their gene products or their downstream partners, researchers could offer a way to fight off infections caused by stress.

While their studies didn’t look at how to gauge the effect of various types of sleep, such as napping or even higher or lower quality rest, their efforts suggest that sleep can help protect against stress-triggered infections.

The total amount and the structure of sleep play roles in this feedback loop. The variability among people makes any broad categorization about sleep needs difficult, as some people function well with six hours of sleep, while others need closer to eight or nine hours per day.

“Scientists are still working out how the brain keeps track of how much sleep it needs to rest and recover,” Borniger explained. “If we can figure this out, then, in principle, we could mess with the amount of sleep one needs without jeopardizing health.”

Researchers don’t know much about the circuitry controlling sleep amount. Borniger recognizes that the conclusions from this study are consistent with what doctors and parents have known for years, which is that sleep is important to overall health. The research also identifies a brain circuit that may be responsible for the way sleep buffers stress and immune responses.

People who have trouble sleeping because of elevated stress from an upcoming deadline often have a flare up of diseases they might have had under control previously, such as herpes viruses or psoriasis. These diseases opportunistically reemerge when the immune system is weakened.

The major finding in this study is not that the connection exists, but that the researchers, including principal investigator Luis de Lecea and first author Shi-Bin Li at Stanford, found the neural components.

While the studies of these linkages in the hypothalamus of mice were consistent across individuals, the same can’t be said for anecdotal and epidemiological evidence in humans, in part because the mice in the study were genetically identical.

For humans, age, sex, prior experiences, diet, family history and other factors make the linkage harder to track.

Even though researchers can’t control for as many variables with humans as they can with mice, however, several other studies have shown that stress promotes insomnia and poor immune function.

Borniger emphasized that he is the second author on the paper, behind Li and was involved in tracking the immune system component of the work.

Borniger and de Lecea are continuing to collaborate to see if drugs that target the insomnia neurons block the effect of stress on the immune system.

Now that he has moved into the refurbished Demerec Laboratory at CSHL, Borniger plans to work on projects to investigate how to use the nervous system to control anti-tumor immunity in models of breast and colorectal cancer, among others.

By understanding this process, Borniger can contribute to ways to manipulate these cells and the immune system to combat cancer and other inflammatory diseases.

Ideally, he’d like to be a part of collaborations that explore the combination of manipulating nervous and immune systems to combat cancer.

Borniger came to Cold Spring Harbor Laboratory because he was eager to collaborate with fellow scientists on site, including those who look at the immune system and metabolism. He appreciates how researchers at the famed research center look at how bodies and the brain respond to a growing tumor and would like to explore how tumors “influence nerves and then, reciprocally, how nerves influence tumor progression.”

The first few steps towards working at CSHL started in 2018, when Tobias Janowitz, Assistant Professor at CSHL, saw a paper Borniger published on breast cancer and asked him to give a 15-minute talk as a part of a young scholars symposium.

Borniger grew up in Washington, DC, attended college at Indiana University, went to graduate school at Ohio State and conducted his post-doctoral work at Stanford. Coming to CSHL brings him back to the East Coast.

Borniger and his fiancée Natalie Navarez, Associate Director of Faculty Diversity at Columbia University, met when they were in the same lab at Stanford. The couple had planned to get married this year. During the pandemic, they have put those plans on hold and may get married at City Hall.

Borniger and Navarez, who live on campus at Hooper House at CSHL, look forward to exploring opportunities to run, hike and swim on Long Island.

The new CSHL researcher appreciates the new opportunities on Long Island.

“This sort of collaborative atmosphere is what I would have in my Utopian dream,” Borniger said.

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James Misewich Photo from BNL

By Daniel Dunaief

Even as the pandemic continues to cast a pall over the prospects for the economy, the federal government is finding ways to support science. Recently, as a part of a $625 billion award to a host of institutions, the Department of Energy earmarked $115 million over five years for a part of a project led by Brookhaven National Laboratory.

The science, called quantum information systems, could have applications in a wide range of industries, from health care to defense to communications, enabling higher levels of artificial intelligence than the current binary system computers have used for decades. By benefiting from the range of options between the 0s and 1s that typically dictate computer codes, researchers can speed up and enhance the development of programs that use artificial intelligence.

The investment “underscores the confidence the federal government has with respect to how important this technology is,” said James Misewich, the Associate Laboratory Director for Energy and Photon Sciences at BNL. “Despite the challenges of the time, this was a priority.”

Local leaders hailed the effort for its scientific potential and for the future benefit to the Long Island economy.

“I have seen strong support inside of Congress and the administration for funding requests coming out of the Department of Energy for ideas on how to move the DOE’s mission forward,” said U.S. Rep. Lee Zeldin (R-NY-1). “I have also seen a very high level of appreciation and respect for BNL, its leadership, its staff, its mission and its potential.”

Zeldin said the average American spends more time than ever engaging with technologies and other discoveries that were made possible by the first quantum revolution. “Here we are on the verge of a second quantum revolution and BNL is at the forefront of it,” Zeldin said.

Zeldin sees limitless possibilities for quantum information science, as researchers believe these efforts will lead to advancements in health care, financial services, national security and other aspects of everyday life. “This next round of quantum advancements seeks to overcome some of the vulnerabilities that were identified and the imperfections in the first wave,” he said.

State Senator James Gaughran (D-Northport) expects quantum science to provide a significant benefit to the region. “We believe this is going to be a major part of our economic future,” he said. “It is a huge victory for Long Island.”

The return on investment for the state and the federal government will also materialize in jobs growth. This is “going to employ a lot of people,” Gaughran said. “It will help to rebuild the type of economy we need on Long Island. The fact that we are on the front lines of that will lead to all sorts of private sector development.”

While the technology has enormous potential, it is still in early enough stages that research groups need to work out challenges before they can fully exploit quantum technology. BNL, specifically, will make quantum error correction a major part of their effort.

As quantum computers start working, they run into a limitation called a noisy intermediate scale quantum problem, or NISQ. These problems come from errors that lower the confidence of getting the right answer. The noise is a current limitation for the best quantum computers. “They can only go so far before you end up with an error that is fatal” to the computing process, Misewich said.

By using the co-design center for quantum advantage, Misewich and his partners hope to use the materials that “beat the NISQ error by having the combination of folks with a great team that are all talking to one another.”

The efforts will use a combination of classical computing and theory to determine the next steps in the process of building a reliable quantum information system-driven computer.

Misewich’s group is also focusing on communication. The BNL scientists hope to provide a network that enables distributed computing. In classical computing, this occurs regularly, as computer scientists distribute a problem over multiple computers.

Similarly, with quantum computing, scientists plan to distribute the problem across computers that need to talk to each other.

Misewich is pleased with the combination of centers that will collaborate through this effort. “The federal government picked these centers because they are somewhat complementary,” he said. The BNL-led team has 24 partners, which include IBM, Stony Brook University, SUNY Polytechnic Institute, Yale University, Princeton University, the Massachusetts Institute of Technology, Harvard University, Columbia University and Howard University, among others.

“We had to identify the best team and bring in the right people to fill the gaps,” Misewich explained.

Using a combination of federal funds and money from New York State, BNL plans to build a new beamline at the National Synchrotron Lightsource II, which will operate at very low temperatures, allowing scientists to study the way these materials work under real word conditions.

BNL would like the work they are doing to have an application in calculations in three areas: the theory of the nucleus, quantum chemistry, which explores ways to design better materials, and catalysis.

A quantum computer could help make inroads in some challenging calculations related to electron-electron interactions in superconducting materials, Misewich said, adding that the entire team feels a “tremendous sense of excitement” about the work they are doing.”

Indeed, the group has been working together for close to two years, which includes putting the team in place, identifying the problems they want to tackle and developing a compelling strategy for the research to make a difference.

The group is expecting to produce a considerable amount of research and will likely develop various patents that will “hopefully transfer the technology so companies can start to build next generation devices,” Misewich said.

Along with local leaders, Misewich hopes these research efforts will enable the transfer of this technology to a future economy for New York State.

This effort will also train a numerous graduate and post doctoral students, who will be the “future leaders that are going to drive that economy,” Misewich said.

The research will explore multiple levels of improvement in the design of quantum computers which they hope will all work at the same time to provide an exponential improvement in the ability of the computer to help solve problems and analyze data.

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Eric Yee. Photo by Felicia Allard

By Daniel Dunaief

In the second of a two-part series, Times Beacon Record News Media will feature the work of Eric Yee, who, like his wife Felicia Allard who was featured last week, is joining the Pathology Department at Stony Brook University.

Eric Yee

Eric Yee, who started as an Associate Professor and Director of Surgical Pathology at Stony Brook Renaissance School of Medicine on July 1, described the focus of his scientific research as translational.

He consults with and helps science researchers put together ideas for experiments, while he and his wife Felicia Allard focus on bringing that work into the clinical setting.

“We provide expertise mainly in clinical gastrointestinal and hepatobiliary pathology,” Yee explained in an email. “We also give insights and perspectives as practicing pathologists to help [with the] analysis of data and how that data in the lab or in animal models may be relevant to clinical medicine.”

Yee completed a gastrointestinal pathology fellowship, working on collaborative research projects and publishing manuscripts with investigators.

As one of the newest members of the staff at Stony Brook, he has worked on some studies looking at certain kinds of inflammatory diseases in the liver. He collaborated with senior investigator Zhenghui Gordon Jiang of Beth Israel Deaconess Medical Center to look at mediators of inflammation in the disease steatohepatitis. He has also worked on different cancer research projects, which is part of the appeal of Stony Brook.

Stony Brook has “important pancreatic research,” Yee said, adding that. Pathology Department Chair Ken Shroyer is a “renowned investigator whose research team has done great work that has led to important insights into pancreatic cancer biology.”

Pancreatic cancer is of particular interest to Yee in his clinical work and he hopes to explore the variety of research expertise at Stony Brook, to support ongoing efforts and to develop projects of his own.

Relocating to Stony Brook from the College of Medicine at the University of Arkansas for Medical Sciences, where Allard and Yee both worked in the Pathology Department, took some convincing for both of the scientists.

“We were very happy in Little Rock and purchased a home in Arkansas two years prior and were just starting to set down roots,” Yee described in an email. “We made lifelong friendships and very much enjoyed the camaraderie among our peers and other departments.”

Yee and Allard had no plans to leave as they approached their third year and were hesitant to move.

In his first visit, Yee said he was impressed with the amount of research in the Stony Brook department, which, he said, has more researchers compared to other institutions of similar size.

On the other side, however, Yee said he and Allard had to reconcile the higher cost of living in New York. They also weren’t eager to make too many moves in their career, especially when they were happy in Arkansas.

Even after the first visit, Yee said he was hesitant to make a move, which would require time to settle in, build relationships, find a home, learn a new system, and find new opportunities, among other challenges..

Shroyer was “very understanding of my hesitation,” Yee explained. “He’s been one of my mentors since medical school and knew exactly where I was coming from.

Clinically, the couple also believed in the potential for career growth.

“There’s a lot of energy in the department,” Yee said. He also appreciated the opportunity to be the Director of Surgical Pathology, where he could shape the operations that support the clinical mission. He would like to optimize the department by specialization, creating a sub-specialty model.

“This is something I want to do to increase the efficiency in the department,” Yee explained. “I’m hoping as we sub-specialize that we make our clinical work flow more efficient” which will create more consistency. “Part of what I’d like to do is to help [Shroyer] create a department where it’ll allow the clinical faculty to thrive.”

Yee thinks any work efficiencies will provide researchers with more time to build on their teaching efforts, and to develop new lectures and teaching models.

Yee will measure his success through a comprehensive report that includes an analysis of the efficiency of the response to clinical needs. He hopes to create a system that will enable the success of the entire anatomic pathology division. He will also become actively engaged in the academic mission, which is measured in the number of publications as well as in staff appointments to editorial boards or major national societies.

“The more people we can get into the national arena the better it is for the institution,” Yee said. These contributions bring good public relations and expertise to the institution.

Yee and Allard will also contribute to Stony Brook through their efforts in education.

Yee believes the school has an advantage in telepathology and distance learning. He believes the Department of Bioinformatics led by Dr. Joel Saltz facilitates telepathology and distance learning.

With the uncertainty caused by COVID-19, Yee believes maintaining social distancing and finding innovative ways for communication and education will provide valuable alternatives to communicate and collaborate.  Radiology has had digital methods in place to send MRIs and CAT scans for a longer period of time than pathologists, who still produce glass slides.

“There will always be some challenges and limitations that are unique to pathology,” Yee suggested.

A native of San Francisco, where he and his older brother, who now works in Boston, grew up, Yee was interested in medicine during the middle of his college career.

Yee and Allard met in medical school and, among numerous other parts of their lives they have in common, discovered they were both fans of the Star Wars films. Early on when they were dating, the pathology couple saw Star Wars: Episode III – Revenge of the Sith together.

Yee enjoys tennis, table tennis, riding road bikes and hiking. He has also developed an appreciation for bird watching, which has allowed him to practice amateur photography.

The couple also shares an interest in music, as Yee grew up playing the piano, while Allard played the trumpet.

When he was in medical school, Yee published his first  paper with Shroyer. He has remained in touch with the pathology chair over the years and appreciates the advice Shroyer has offered.

Yee described Shroyer as an “inspirational leader” and appreciates his energy, selflessness and passion, among other qualities.

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the U.S. Department of Energy awarded a 10-year multi-billion project to build a new electron-ion collider at Brookhaven National Laboratory in Upton. Provide photo from Brookhaven National Lab

By Daniel Dunaief

Through answers to basic questions, scientists develop new technology that changes the world, leading to medical breakthroughs, energy applications and national security devices.

That’s the theory behind the U.S. Department of Energy’s decision last week to award a 10-year project that will cost between $1.6 billion and $2.6 billion to build a new electron-ion collider at Brookhaven National Laboratory in Upton. 

For the scientists, the discoveries will flow from answers to questions about the nature of visible matter.

“The big science we’re excited about, the hundred-year-old questions, are things like where does the mass of a proton come from,” said Robert Tribble, the deputy director for science and technology at Brookhaven National Laboratory and a nuclear physicist. The EIC is like a microscope to look at quarks and gluons, he explained.

With support from numerous New York State and Long Island leaders, BNL recently won a competition against Thomas Jefferson National Accelerator in Virginia to build an electron-ion collider. Members of the Jefferson Accelerator, as well as over 1,000 scientists from 30 nations, will partner with BNL staff to conceptualize and build the new collider, which will be the most advanced ever constructed.

In addition to understanding atomic nuclei, we will be able to generate a better view of the universe writ large [with discoveries from the EIC].”

– Robert Tribble

“We do not understand very dense matter that exists in the universe in objects like neutron stars and black holes,” Tribble explained in an email. “In addition to understanding atomic nuclei, we will be able to generate a better view of the universe writ large [with discoveries from the EIC].”

Over the next decade, the construction of the new EIC will employ 4,000 people, said Doon Gibbs, the laboratory director at BNL. That number represents the workforce that will, at one time or another, contribute to the construction of this new facility. 

The new EIC will expand on the technology of the Relativistic Heavy Ion Collider, which has been operating since 2000 and will stop running experiments in 2024. Indeed, part of the appeal of BNL as a site for this new facility arose out of the ability to extend the resources by building a new electron storage ring and electron accelerator elements.

Researchers will collide electrons and protons and numerous atomic nuclei to study the strong nuclear force. These collisions will reveal how the subunits of protons and neutrons in the nucleus, namely the quarks and gluons, come together to help generate mass in visible matter.

The staff at BNL is “delighted and excited” that the site for the EIC will be on Long Island, said Gibbs. “Our design has the capability of using many existing technologies and extending them farther than they’ve been before.”

Indeed, even the conception of the EIC has led to some new scientific breakthroughs, some of which the lab and its partners will share with the public in the next few weeks.

While the application of research at the EIC will likely lead to breakthroughs in fields including materials science, researchers at BNL are excited about basic questions about the nature of nuclear matter.

A typical experiment at the EIC will likely follow the same pattern as it has with RHIC, in which hundreds of researchers from around the world collaborate to understand physics properties. In the next few years, researchers will develop a detailed design before they start construction.

“We love challenges at BNL, we like building big machines. We’re good at it. We have a whole class of staff who, in particular, are experts at this kind of activity and they are pretty excited.”

– Doon Gibbs

Gibbs said the facility has a strong handle on the safety features of the new collider, which will build on the protocols and designs developed at the RHIC as well as with the National Synchrotron Light Source II, also at the lab in Upton.

“We love challenges at BNL,” Gibbs said. “We like building big machines. We’re good at it. We have a whole class of staff who, in particular, are experts at this kind of activity and they are pretty excited.”

Area politicians are also excited about discoveries in basic science, translational benefits in areas like medicine and the expected boost to the local economy.

“Establishing the electron-ion collider on Long Island might be focused on particles, but it will add some serious mass — nearly $1 billion worth — to the local economy,” U.S. Sen. Chuck Schumer (D) said in a statement. BNL has the “talent, the technology and the track record to make the most of this national project.”

Schumer believes this project will guarantee that BNL continues to be a “world class research facility for the next generation.”

U.S. Rep. Lee Zeldin (R-Shirley) praised the leadership at BNL.

“I congratulate BNL Director Doon Gibbs for leading this exceptional organization and all of its scientists who have worked incredibly hard every step of the way to make this possible, and can’t wait to see what they do next,” Zeldin said in a statement.

 

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Nicholas Gladman with a harvest of sorghum at Cornell University’s Long Island Horticultural Research Lab in Riverhead. Photo by Sendi Mejia

By Daniel Dunaief

When people buy a bag of potato chips, they often find that half of the bag is filled with air. The same is true of a sorghum plant, which produces livestock feed and is converted into ethanol, part of many gases that power cars.

Nicholas Gladman

In a typical sorghum plant, half of the flowers become grain, while the other half remain infertile. As the world grapples with food shortages and scientists seek ways to increase the yield of a wide array of plants, researchers at Cold Spring Harbor Laboratory wondered whether they could increase that yield.

Building on previous work done in the lab of Doreen Ware, an adjunct professor at CSHL, postdoctoral fellow Nicholas Gladman characterized a mutation for a single gene that lowered the level of a hormone. The effect of the lower hormone, or jasmonic acid, at a specific time and place within plant development doubled the fertility of the sorghum plant.

“When we don’t have a functional version of this enzyme, it releases this form of development that wouldn’t normally occur,” Gladman said. “You get increased fertility in flowers.”

The gene they studied is called MSD2. The researchers published their work in International Journal of Molecular Sciences. Another gene, MSD1, which Ware’s lab characterized in 2018, is a likely regulator for MSD2. Other genes may also serve as regulators of MSD2, Gladman said. Disruptions in either gene leads to altered flower development and seed production.

Gladman’s postdoctoral research adviser Zhanguo Xin collaborated on the work. Xin, who is a research molecular biologist at the United States Department of Agriculture’s Agricultural Research Service, explained that Gladman characterized the mutants, identified the interaction between MSD1 and MSD2 and identified the regulatory sequences of MSD1.

This research could extend to other cereal crops, which have the same conserved sets of genes that affect their growth and fertility.

A concern in altering any gene resides in the overall effect on the health of the plant. Creating a super plant that falls over and dies in a slight wind, can’t fend off common infections, or requires a perfect blend of soil would likely offset the benefit of the increased fertility. Plant geneticists would like to ensure any mutation doesn’t make the plant less viable in the long run.

“Sometimes there can be a trade off between an agriculturally beneficial genetic change by introducing other detrimental effects,” Gladman explained in an email. “Optimally, plant geneticists will try to ensure the side effects of any mutation are insignificant to farmers; sometimes, this is more difficult and the downsides may not always present themselves at the early stages of lab investigation.”

This particular gene is narrowly and spatially expressed within the plant, Gladman said, and the researchers haven’t been able to identify or quantify the effect of this gene on anything else other than flowers and floral architecture.

The gene and the hormone would be a concern if it were expressed more broadly and at high levels throughout other plant tissues, but that doesn’t seem to be the case, he said.

The researchers have looked at other tissues, such as the leaf and stem, and have found that MSD2 is expressed in low levels in these other areas. Plants that have the MSD2 mutation do not demonstrate any noticeable differences in growth compared to nonmutants in the field or in greenhouse conditions. If this mutated gene had an agricultural benefit, farmers would likely crossbreed a plant that had this gene with an elite sorghum hybrid line

Ideally, the benefits of the increased fertility would combine with benefits of all the genetic components of the hybrid lines as well. The way the researchers involved in this study produced this more fertile version of sorghum is an “acceptable type of breeding for organic or conventional farming,” Gladman said.

While the plant increases the grain number per seed head, it doesn’t necessarily produce greater overall yield in part because the seeds are smaller. Researchers haven’t been able to confirm that yet in a field condition, although they hope that’s the case.

Gladman was grateful for the opportunity to work in Ware’s lab and to collaborate with Xin. The effects of disrupting similar genes in maize and Arabidopsis, which is a plant in the mustard family that scientists often use in genetic studies, influences flower fertility.

He said researchers in Ware’s lab can perform additional developmental analysis. The researchers in Ware’s lab may seek additional collaborators for other analyses down the road as well.

“How this particular pathway is triggered and cross-communicates with other developmental pathways is very complex, but influences so much about traits that control grain production and yield that it is essential for further investigations,” he explained.

Gladman arrived at Cold Spring Harbor Laboratory in 2017. Prior to conducting research on Long Island, he finished his doctorate at the University of Wisconsin at Madison, where he worked on Arabidopsis. He decided he wanted to get more involved with crop species and explored research opportunities at United States Department of Agriculture labs. He was working with Xin in Lubbock, Texas, before transitioning to Cold Spring Harbor Laboratory.

Gladman has been delighted by the “wonderful place to learn,” where he is surrounded by “people who are always willing to talk and engage and collaborate.”

A resident of Greenlawn, Gladman enjoys hiking along the Hudson and in the Adirondacks. He credits a high school biology class he took in Grandview Heights High School in Columbus, Ohio, with instilling in him and his three brothers an appreciation and love of science. He particularly enjoyed a unit on the “genetics of disease” that inspired him to pursue a career in the sciences.

As for his work, Gladman is excited to be a part of research that may, one day, increase the productivity of crop species. He said thoughts about food shortages are “a constant concern and driver of our research.”

 

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Interns Nylette Lopez (rear) and Stephanie Taboada characterize catalysts as they attempt to convert carbon dioxide and methane into synthesis gas this past summer at Brookhaven National Laboratory. Photo from BNL.

By Daniel Dunaief

This article is part two in a two-part series.

Local medical and research institutions are aware of the challenges women face in science and are taking steps to ensure that women receive equal opportunities for success in science, technology, engineering and mathematics (or STEM). Times Beacon Record News Media reached out to members of each institution and received an overview of some initiatives.

Brookhaven National Laboratory 

The Department of Energy-funded research facility has created a number of opportunities for women, including Brookhaven Women in Science. This effort has been active for over four decades and its mission, according to Peter Genzer, a BNL spokesman, is to support the development of models, policies and practices that enhance the quality of life for BNL employees and emphasize the recruitment, hiring, promotion and retention of women.

BWIS offers annual awards, outreach events and various networking opportunities in the lab and community, while the lab’s Talent Management Group partners with BWIS to bring classes and speakers to discuss issues specific to women.

In October, the group hosted Kimberly Jackson, a vice chair and associate professor of chemistry and biochemistry at Spelman College, who gave a talk titled “Realigning the Crooked Room in STEM.”

The Leona Woods Distinguished Postdoctoral Lectureship Award at BNL, meanwhile, celebrates the scientific accomplishments of female physicists, physicists from under-represented minority groups and LGBTQ physicists and to promote diversity and inclusion. BNL awarded the lectureship this year to Kirsty Duffy, a fellow at Fermi National Accelerator Laboratory.

For the past five years, BNL has also partnered with a local chapter of Girls Inc., which helps to “encourage young women towards careers” in STEM, Genzer explained in an email.

BNL has also collaborated with the Girl Scouts of Suffolk County to organize a new patch program that encourages Girl Scouts to work in scientific fields. As of September, county Girl Scouts can earn three new Brookhaven Lab patches, and the lab hopes to extend the program nationwide across the Department of Energy complex.

BNL also provides six weeks of paid time off at 100 percent of base pay for a primary caregiver after birth or adoption and one week of full pay for a secondary caregiver. BNL is exploring plans to enhance support for primary and secondary caregivers, Genzer said.

Cold Spring Harbor Laboratory

Cold Spring Harbor Laboratory has taken several recent steps as part of an ongoing effort to encourage gender diversity.

In October, a group of four CSHL administrators traveled to the University of Wisconsin in Madison to discuss mentoring. The goal was to train them on how to design and deliver mentoring training regularly to the faculty, postdocs and graduate students on campus, said Charla Lambert, the diversity, equity and inclusion officer for research at CSHL. The first version of the training will occur next spring. The ultimate goal is to ensure the research environment at CSHL emphasizes good mentoring practices and is more inclusive for all mentees.

CSHL has also hosted a three-day workshop in leadership practices for postdoctoral researchers and junior faculty since 2011. The workshop, which is run through the Meetings & Courses Program, trains about 25 postdoctoral researchers and junior faculty each year and has about one per year from CSHL, addresses how to hire and motivate people, while providing constructive feedback.

Lambert said family-friendly policies were already a part of CSHL policies, which include a child care facility. Members of the faculty receive extra funding when they travel to conferences to provide additional child care.

Lambert, who is a program manager for extramural Meetings & Courses overseeing diversity initiatives, has worked to get the demographic data for participants centralized, analyzed and used in developing policies. She believes this kind of data centralization is an area for potential improvement in the research division, where she is working to ensure an equitable distribution of resources among CSHL scientists.

Throughout her nine-year career at CSHL, Lambert said she has worked with the meetings and courses division to make sure the 9,000 scientists who visit the facility each year include women as invited speakers. She also works to reach course applicants from a wide range of institutions, including outside of prestigious research schools.

Ultimately, Lambert is hoping to help change the culture of science among the researchers with whom she interacts from a wide range of institutions. She feels that those people who leave the STEM fields because something about the culture of science didn’t work for them represent a “huge loss” to the field and creates a “survivorship bias.”

Stony Brook University 

For Stony Brook, gender diversity is “very important,” said Latha Chandran, the vice dean for Academic and Faculty Affairs at the Stony Brook University Renaissance School of Medicine. 

Chandran said more men entered the field of medicine 14 years ago. That has completely changed, as women have outnumbered their male counterparts in medicine for the last three or four years.

Chandran cited a number of statistics to indicate changes at the medical school. For starters, women faculty constituted 38 percent of the total in 2011. This April, that number climbed to 48.1 percent. That puts Stony Brook in the top 79th percentile of medical schools in terms of female representation.

While the overall numbers are higher, women are still underrepresented in the top tiers of the medical school, as 18 percent of the department chairs are women. She hopes more women can lead departments and that they can serve as role models that others can aspire to follow.

As for harassment, Chandran said Stony Brook was above the national mean in 2011. For almost all categories, Stony Brook is now below the national mean.

In 2011, Stony Brook created We Smile, which stands for We can Eradicate Student Mistreatment in the Learning Environment. The goal of this program is to educate people about harassment and to ensure that any mistreatment is reported. Through this effort, Stony Brook medical students are aware of the policies and procedures surrounding reporting.

Stony Brook is also addressing any bias in admission procedures by prospective applicants, who receive a standardized scenario to address with an admissions officer. In 2025, admissions officers will not have any information about the qualifications of the individual and will evaluate his or her response during interviews only based on response to scenarios.

Stony Brook University has almost finalized its search for a chief diversity candidate. Chandran expects that the medical school will “continue to make progress.”

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Peter Koo. Photo by ©Gina Motisi, 2019/ CSHL

By Daniel Dunaief

We built a process that works, but we don’t know why. That’s what one of the newest additions to Cold Spring Harbor Laboratory hopes to find out.

Researchers have applied artificial intelligence in many areas in biology and health care. These systems are making useful predictions for the tasks they are trained to perform. Artificial intelligence, however, is mostly a hands-off process. After these systems receive training for a particular task, they learn patterns on their own that help them make predictions.

How these machines learn, however, has become as much of a black box as the human brains that created these learning programs in the first place. Deep learning is a way to build hierarchical representations of data, explained Peter Koo, an assistant professor at the Simons Center for Quantitative Biology at CSHL, who studies the way each layer transforms data and the next layer builds upon this in a hierarchical manner.

Koo, who earned his doctorate at Yale University and performed his postdoctoral research at Harvard University, would like to understand exactly what the machines we created are learning and how they are coming up with their conclusions.

“We don’t understand why [these artificial intelligence programs] are making their predictions,” Koo said. “My postdoctoral research and future research will continue this line of work.”

Koo is not only interested in applying deep learning to biological problems to do better, but he’s also hoping to extract out what knowledge these machines learn from the data sets to understand why they are performing better than some of the traditional methods.

“How do we guide black box models to learn biologically meaningful” information? he asked. “If you have a data set and you have a predictive model that predicts the data well, you assume it must have learned something biologically meaningful,” he suggested. “It turns out, that’s not always the case.”

Deep learning can pick up other trends or links in the data that might not be biologically meaningful. In a simplistic example, an artificial intelligence weather system that tracked rain patterns during the spring might conclude, after seven rainy Tuesdays, that it rains on Tuesdays, even if the day of the week and the rain don’t have a causative link.

“If the model is trained with limited data that is not representative, it can easily learn patterns that are correlative in the training data,” Koo said. He tries to combat this in practice by holding out some data, which is called validating data. Scientists use it to evaluate how well the model generalizes to new data.

Koo plans to collaborate with numerous biologists at Cold Spring Harbor Laboratory, as well as other quantitative biologists, like assistant professors Justin Kenney and David McCandlish.

In an email, Kenney explained that the Simons Center is “very interested in moving into this area, which is starting to have a major impact on biology just as it has in the technology industry.”

The quantitative team is interested in high-throughput data sets that link sequence to function, which includes assays for protein binding, gene expression, protein function and a host of others. Koo plans to take a “top down” approach to interpret what the models have learned. The benefit of this perspective is that it doesn’t set any biases in the models.

Deep learning, Koo suggested, is a rebranding of artificial neural networks. Researchers create a network of simple computational units and collectively they become a powerful tool to approximate functions.

A physicist by training, Koo taught himself his expertise in deep learning, Kenney wrote in an email. “He thinks far more deeply about problems than I suspect most researchers in this area do,” he  wrote. Kenney is moving in this area himself as well, because he sees a close connection between the problem of how artificial intelligence algorithms learn to do things and how biological systems mechanistically work.

While plenty of researchers are engaged in the field of artificial intelligence, interpretable deep learning, which is where Koo has decided to make his mark, is a considerably smaller field.

“People don’t trust it yet,” Koo said. “They are black box models and people don’t understand the inner workings of them.” These systems learn some way to relate input function to output predictions, but scientists don’t know what function they have learned.

Koo chose to come to Cold Spring Harbor Laboratory in part because he was impressed with the questions and discussions during the interview process.

Koo, daughter Evie (left) and daughter Yeonu (right) during Halloween last year. Photo by Soohyun Cho

He started his research career in experimental physics. As an undergraduate, he worked in a condensed matter lab of John Clarke at the University of California at Berkeley. He transitioned to genomics, in part because he saw a huge revolution in next-generation sequencing. He hopes to leverage what he has learned to make an impact toward precision medicine. 

Biological researchers were sequencing all kinds of cancers and were trying to make an impact toward precision medicine. “To me, that’s a big draw,” Koo said, “to make contributions here.”

A resident of Jericho, Koo lives with his wife, Soohyun Cho, and their 6-year-old daughter Evie and their 4-year old-daughter Yeonu.

Born and raised in the Los Angeles area, he joined the Army Reserves after high school, attended community college and then transferred to UC Berkeley to get his bachelor’s degree in physics.

As for his decision to join Cold Spring Harbor Laboratory, Koo said he is excited with the opportunity to combine his approach to his work with the depth of research in other areas. 

“Cold Spring Harbor Laboratory is one of those amazing places for biological research,” Koo said. “What brought me here is the quantitative biology program. It’s a pretty new program” that has “incredibly deep thinkers.”

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