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Symposium Report: Stanford One Health Focus on Comparative Oncology

Event Details:

Stanford One Health 2017: Focus on Comparative Oncology

May 8, 2017

Frances C. Arrillaga Alumni Center


Report prepared by:

Ashley Zehnder, DVM, PhD, ABVP (Avian)

Stanford Department of Biomedical Data Science

Co-Director, Stanford One Health

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Report Contents:

  1. Mission/Goals
  2. Meeting format
  3. Conference speakers with bios
  4. Demographics of attendees
  5. Potential new collaborations
  6. Conference evaluations
  7. Future plans

Mission/Goals:

The purpose of Stanford One Health: Focus on Comparative Oncology was to connect Stanford clinicians and researchers to cutting-edge comparative research and resources in order to aid the translation of basic science cancer discoveries to the clinic.

We expected that this focused symposium would produce:

  • New collaborations and novel hypotheses for investigations around translational cancer research.
  • Potential for new approaches to the diagnosis and treatment of disease in both animals and humans.

This conference emerged as a continuation of other Stanford One Health symposia, held in 2014 (http://med.stanford.edu/compmed/zoobiquity.html) and 2016 (http://med.stanford.edu/compmed/one-health-2016.html), that focused on a broad range of topics. The main organizers of SOH 2017 were Ashley Zehnder, DVM, PhD, DABVP(Avian), a research scientist in the Department of Biomedical Data Science with a focus on comparative oncology research, and Donna Bouley, DVM, PhD, DACVP, and Jose Vilches-Moure, DVM, PhD, DACVP, pathologists in the Stanford Comparative Medicine Department.

Meeting Format:

The symposium began at 9:00 AM and concluded at 3:30 PM. We opened with an introduction by organizer Ashley Zehnder and Dr. Carlos Bustamante, Inaugural Chair of the Department of Biomedical Data Science. The morning session consisted of four veterinary oncology speakers, highlighting different translational cancer programs from around the country, including Colorado State University, the University of California, Davis, the University of Minnesota, and the NIH Comparative Oncology Trials Consortium.

The afternoon session consisted of a focused discussion panel on four topics:

  1. Areas of collaboration between Stanford and the comparative oncology community;
  2. Ways in which a more collaborative approach to translational research can help Stanford researchers develop novel therapies;
  3. Potential funding sources for collaborative research projects;
  4. Ways to engage Stanford trainees (MD, PhD, postdocs) in comparative oncology.

[Discussion transcripts and whiteboard notes pending]

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SOH2017 Attendees

Speakers and Bios:

Rodney Page, Professor and Director of the Flint Animal Cancer Center, Stephen Withrow Presidential Chair in Oncology, College of Veterinary Medicine and Biomedical Sciences, Colorado State University

Dr. Page received his DVM from Colorado State University and completed specialty training in the field of medical oncology in NYC.  He was a faculty member at North Carolina State University, prior to his appointment at Cornell University as Founding Director of The Sprecher Institute for Comparative Cancer Research. In 2005, Dr. Page was appointed Chair of the Department of Clinical SciencesDr. Page returned to Colorado as the Director of the Flint Animal Cancer Center in 2010 (www.csuanimalcancercenter.org).  His research interests have recently been focused on a ‘One Medicine’ approach to cancer. He has been involved with the Golden Retriever Lifetime Study since 2008, and has initiated a national effort to bring translational and comparative oncology to a greater audience. Website 

Antonella Borgatti, Associate Professor, Department of Veterinary Clinical Sciences, University of Minnosota

Dr. Borgatti graduated cum laude from the University of Torino, Italy in 1996. After three years in general practice, she received a scholarship to pursue specialized training in oncology at North Carolina State University, where she subsequently remained as a Research Associate, Oncology Intern, and Clinical Instructor in Oncology. She completed a Residency in Comparative Oncology at Purdue University, where she also received a Master of Sciences Degree in 2006. Dr. Borgatti became a Diplomate of the American College of Veterinary Internal Medicine (Oncology) in 2006, and a Diplomate of the European College of Veterinary Internal Medicine in 2007. She worked at a specialty referral hospital in North Carolina for two years before joining the faculty at the University of Minnesota in 2008. She is currently Associate Professor of Oncology in the College of Veterinary Medicine, Member of the Masonic Cancer Center, Member of the Vallera laboratory, and Director of the Oncology residency program. Website

Michael Kent, Director of the Center for Companion Animal Health, UC Davis

Michael Kent is a Professor of Radiation Oncology at the University of California, Davis’s School of Veterinary Medicine. He is also Director of the Center for Companion Animal Health. He graduated from veterinary school at UC Davis in 1997. He then went on to do an internship at the University of Pennsylvania. This was followed by a year in private practice in Pennsylvania before he went on to do residencies in Medical and Radiation Oncology at UC Davis, where he also received his Masters Degree in clinical research. He is also the program co-leader for the comparative oncology program at the medical school’s NCI-designated comprehensive cancer center. His research interests include clinical trials and tumor biology of canine melanoma and osteosarcoma. Website

Amy LeBlanc, Director, Comparative Oncology Program, NIH

Dr. LeBlanc is a board-certified veterinary oncologist and Director of the CCR Comparative Oncology Program at the NIH’s National Cancer Institute. In this position, she directly oversees and manages the operations of the Comparative Oncology Trials Consortium (COTC), which designs and executes clinical trials of new cancer therapies in tumor-bearing pet dogs. Her research focuses on animal modeling for the development of new cancer drugs and imaging agents, and identification of imaging biomarkers, development, and optimization of PET imaging hardware and imaging protocols. She has experience in fostering collaborations with industry and academic partners to support relevant eIND studies in man. She has given numerous invited lectures on the inclusion of companion animals in imaging-based translational research, and the value of comparative oncology in drug and imaging agent development. Website

Demographics of attendees (Including speakers and organizers):

Conference attendance was capped at 45 to allow for more active discussion and interactions between speakers and participants. There were 44 pre-registered attendees and a total of 32 final attendees.

Degree Total % Total
DVM 2
DVM/MD 1
DVM/Board Certification 9
DVM/PhD 1
DVM/PhD/Board 3
Total DVM 16 48.5%
MD 1
MD /PhD 3
Total MD 4 12.5%
PhD/PhD Cand 6 18.8%
Other (NP) 1 3.1%
Not Stated 5 15.6%
Total 32 100.0%

New collaborations from the meeting:

Collaborator1 Institution1 Collaborator2 Institution2 Project/topic
Bryan Smith Stanford Michael Kent UC Davis Molecular imaging
Ashley Zehnder Stanford Michael Kent UC Davis Veterinary data science
Kevin Grimes Stanford Antonella Borgatti UMN Cancer drug translation
Teresa Purzner Stanford Michael Kent UC Davis Osteosarcoma
Jianghong Rao Stanford Amy Leblanc NIH NCI PET imaging agents
Juergen Willmann Stanford Amy Leblanc NIH NCI Molecular imaging
Carlos Bustamante Stanford Rod Page CSU Bioinformatics training program

Several new collaborations are being explored following this meeting between the invited speakers and researchers at Stanford, including research focused on molecular imaging, veterinary data science and bioinformatics, cancer drug translation and osteosarcoma research.

Evaluations (quantified results pending): 

Conference feedback was all very favorable, especially regarding the symposium content and speakers. Everyone from Stanford who has provided feedback, thus far, has supported the development of a formal One Health program at Stanford.

Future Plans: 

We are very pleased with the success of all three “One Health”-themed conferences (the Stanford Zoobiquity Research Symposium 2014, One Health 2016, and the 2017 focused symposium on Comparative Oncology). The Stanford One Health Advisory board is currently working on a proposal for a formal One Health Center for the University’s long-range planning process.

 

 

Feature Interview: Dr. Plavi Mittal, Founder & CEO, In-Depth Diagnostics

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Dr. Plavi Mittal earned her Ph.D. in Biology from Brandeis University, and did her postdoctoral research in molecular oncology at Harvard Medical School. She was also a management consultant at a global consulting firm, where she worked with leading pharmaceutical companies.

After a family member was diagnosed with a rare muscular dystrophy, LGMD2B/Miyoshi, Dr. Mittal helped create the Jain Foundation. Over the last 12 years, she has led the JF team as President & CEO, and together, they partnered with dysferlinopathy researchers to realize gene therapy clinical trials and the hope for a cure. Repeatedly, Dr. Mittal has seen patients with rare disease struggle to reach a diagnosis and find a treatment best for them, despite the scientific breakthroughs advancing therapies for their condition.

Through her new non-profit organization based in Seattle, Washington, In-Depth Diagnostics [www.indepthdiagnostics.org], Dr. Mittal will continue to support the mission of the Jain Foundation while addressing this larger patient need by providing genome-level sequencing and analysis. IDD’s national diagnostic program is an unprecedented effort that will raise standards for diagnosing rare diseases and also fuel a research consortium focused on improving clinical care.

Can you tell us more about your background before starting the Jain Foundation? How did you first become interested in science, biology, and oncology?

I was always interested in Genetics and Biology for as far back as I remember. I think my interest started when I read the book, Lives of a Cell by Lewis Thomas. I was fascinated with the diversity, the resilience and the complexity of biological organisms. Later, as a PhD student, I was very keen to work on problems that would impact people suffering from diseases today. I feel that we have an urgent mission to connect the dots from everything we have already learned.

Can you tell us about your work at the Jain Foundation over the past decade, and how that led you to start In-Depth Diagnostics (IDD)? 

At the Jain Foundation, we were completely focused on pushing research towards a cure for LGMD2B, a rare form of muscular dystrophy. Over the years, our strategy of uniting researchers with the relevant expertise proved successful, and we set the stage for clinical trials. Then, I learned first-hand what industry has been struggling with for years: rare diseases are difficult to research, because the patients needed for clinical trials are very difficult to find. With the hopes of finding enough patients to develop a meaningful trial for LGMD2B, the Jain Foundation developed a free diagnostic program. We put together a panel of 35 genes linked with diseases that would have a similar presentation as our disease of interest, LGMD2B. We were able to screen 2,500 people and diagnose dozens of LGMD2B patients. This work confirmed my belief that genetic testing is a quick and efficient clinical tool for complex diagnostic cases.

What convinced you that there is a need for better diagnostics for rare diseases? Why is diagnosis so important for these patients?

While the diagnostic program was very successful at finding LGMD2B patients for the Jain Foundation patient registries, over 60% of the patients tested received no diagnosis. I felt a personal dedication to these patients who were offered the hope of an answer, only to be let down by the inherent limitations of a panel-based approach. These patients would have to wait many more months while they sought other opportunities for genetic testing, if they had the resources to do so. Given the falling price of human genome sequencing and clinical analysis, performing one thorough analysis seemed to me to be more efficient and effective than repeated genotyping. By focusing on providing comprehensive genetic analysis to these patients, I have the opportunity to provide an under-utilized, powerful diagnostic tool to patients in critical need of targeted treatment plans. And by empowering patients with their genetic diagnosis, patients can seek out research and clinical trials best suited to their condition.

How did you choose whole genome sequencing, and how does this open up new avenues for research?

By performing whole genome sequencing, we will be assessing as much of the human genome as technology currently allows. This means that, in addition to identifying known pathogenic variants for diagnostic purposes, we will be able to uncover nuanced patterns in other regions of the genome. We hope that, by strategically combining our bioinformatic analysis with information about patients’ symptoms and traits, we can highlight promising avenues for therapy development for a great number of rare neurological diseases.

What do you think distinguishes IDD from other genetic testing/analysis/diagnosis services available today? Why do you think now is the right time for IDD to open its doors?

I’ve been considering this very question for months – right now, the clinical and academic applications of genomics are booming. So many groups and companies are launching large projects or consumer products that the market appears saturated with personalized technology. However, as I’ve built IDD’s program, it has become painfully clear that the vast majority of commercial products are not able to offer a clinical diagnosis to patients seeking one, or they do not perform a full genome analysis at all. Many insurance plans do not cover comprehensive genetic testing, and patients cannot afford to pay out of pocket for this additional test when they are facing a myriad of diagnostic procedures. By offering our services to patients at no charge, and performing full genome sequencing/analysis for clinical and research applications, we are the only program working to deliver this cutting edge technology directly to patients who could benefit most.

What is your vision for In-Depth Diagnostics going forward?

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My vision is for In-Depth Diagnostics to become a leader in rare disease diagnosis and patient engagement. By gathering evidence supporting the efficiency of genetic screening for difficult-to-diagnose neurological conditions, I hope to influence a shift in clinical standards of practice. I don’t plan to measure the success of my program only by the number of patients diagnosed; my success is also contingent on creating an accessible community where patients can learn about the unique ways patient participation can accelerate and influence the development of rare disease therapies. By empowering patients and generating sufficient data, I hope IDD’s program will spark therapy development for a number of rare conditions.

What directions do you see genomic testing (including analysis, diagnosis, and counseling) taking in the future? Do you see a lot of change happening in this area? Do you think these changes are positive or negative? Why?

I think we are rapidly moving to the era of unlocking all of DNA’s mysteries, and really charging forward and diagnosing most conditions in much less time. I am not as sure that we, as a species, will take care to provide adequate support, guidance and counseling along with the diagnosis. I hope we do, and IDD is definitely striving for that deep level of engagement with the patient, becoming a source of support for them.

The changes unlocking of the DNA will bring to diagnosis is a big step forward in the right direction. Everything starts with diagnosis: by naming the suffering – then we can begin to understand the origins and begin to develop treatments.

How can members of the CEHG community get involved with In-Depth Diagnostics?

Once sufficient data is collected, IDD hopes to launch a major research effort that will combine groups across academia and industry who are studying human disease, developing therapies, or performing other computational biology projects that may benefit from data such as ours. Any researcher from the CEHG community who is interested in working with IDD’s curated database should contact the foundation for application.

CEHG’s core values are “collaboration” and “interdisciplinarity.” Are there ways you hope IDD will embody these values as well?

Absolutely! While genomic data is at the heart of this program, I know that progress in clinical care for rare diseases will only occur after combining data from numerous other health factors and biological perspectives. To put our program’s data to the best use, we must rely on collaborations with groups across industry and academia to elaborate on relevant findings and push the genetic information towards a meaningful application.

What advice would you give to early career scientists, having worked in both academia and at foundations with a patient-centric focus?

My advice is to always look 10 steps ahead and find the connection to how your research will help humans. This exercise makes everything so much more focused, and also very meaningful.

What advice would you give to patients?

Advocate for yourself; there are answers your doctor may not know. Participate in all aspects of drug development. Read and get educated about your disease.

Fellows Feature: Ryan York

Ryan York_ForWeb

Ryan York is a CEHG graduate fellow in the labs of Russell Fernald and Hunter Fraser. He is a graduate of the University of California at Los Angeles. His research is focused on the evolutionary genomic basis of brain and behavior, with a specific interest in the courtship behaviors of Lake Malawi cichlid fish.

Can you tell us a bit about yourself, personally and professionally?

I am a graduate student in the labs of Russell Fernald and Hunter Fraser. I grew up in the Bay Area, and did my undergrad at UCLA. Before coming to Stanford, I worked as a research technician, first in Stephanie White’s lab at UCLA, studying the molecular bases of bird song, and then with John Allman at Caltech, researching neural traits unique to humans. My research is broadly concerned with understanding the evolution of brains and behaviors across disciplines, from genes to organisms. I am also a musician and artist and am interested in the intersections of art and biology.

Did you always want to be a scientist? What initially got you interested in science and genetics?

I didn’t always want to be a scientist. I was not someone who, as a child, knew they were destined to study a specific species or natural phenomenon. In fact, I began my undergraduate years as a Jazz Studies Major, having semi-professionally performed and recorded as a double bassist since the age of 14. What’s more, in high school, I was a “bad” science student, constantly feeling like I couldn’t measure up to those in my class who seemed to show natural talent for understanding and memorizing facts about enzymatic reactions and taxonomy. I was interested, but disengaged, convinced that my future lay in the Arts. Yet when I began taking classes in history and sociology in college, I realized that a whole world of interest existed for me outside of art. I caught the bug of wanting to understand human behavior, and that drive led me to crave more and more fundamental levels of understanding. Sociology led me to psychology, psychology led me to neuroscience, and neuroscience led me to genetics and molecular biology, and ultimately to where I am now.

Can you tell us about your current research and what you want to achieve with it?

My current research is focused on investigating how genomes produce the great behavioral diversity observed in animals. Despite decades of research, we still don’t fully understand how variation in genes and their regulation changes the function of the brain and its main output, behavior (especially our own). Historically, this has been due to technological constraints that incentivized researchers to focus on just a few model systems and behavioral types. Recent innovations in sequencing, neurobiology, and behavioral analysis are now allowing behavioral biologists to expand their focus to new species and groups displaying extreme behavioral diversity. My work attempts to develop methods that integrate these new approaches in order to understand how behaviors evolve and vary across biological levels.

I am primarily focused on an extremely diverse group of fish (cichlids) from Lake Malawi in East Africa. Though Lake Malawi is only around 5 million years old (i.e. very young, geologically speaking), there are already over 800 species of Malawi cichlids. Over 100 of these species perform a mating behavior, called “bower building,” that I am particularly interested in. During breeding season, males of these species will competitively build 3D structures out of sand to attract females, either in the form of a classic “sand castle” or as an excavated depression we a call a “pit”. We have shown that whether or not a male builds a castle or a pit is species-specific and innate, and that if you hybridize a pit species and castle species, the resulting hybrids will build both structures, resulting in a “pit-castle” bower.

To understand the genetic basis of this behavior, I am combining whole genome sequencing and RNA-seq in the hybrids, to uncover variants affecting the regulation of neural genes during different behavioral states. I am also using high-throughput behavioral phenotyping and genetic methods for analyzing signatures of recent neural activity to understand how variation in the cichlid genome leads to different behavioral and neural traits. I am now also working on applying these genetic methods to other types of data and species, including deer mice and fruit flies.

Were there specific people to whom you would attribute your academic and professional success?

There have been various people in my life who have had substantial impacts on my path (though not necessarily in ways that would lead one to predict that I’d end up in science). First off, my family has always been very supportive of whatever I wanted to pursue, be it jazz or evolutionary genetics, and have, at least, attempted to always show real interest in the odd topics I get obsessed with. In high school, my bass teacher, Seward McCain, supported my desire to major in music in college, but also strongly advocated for getting a full education outside of music, in order to avoid being one dimensional.

Multiple people in the sociology and anthropology departments at UCLA – Andrew Deener, Doug Hollan, Zsuzsa Berend, Jeffrey Prager, Alan Fisk – were instrumental in helping me figure out my life outside of music, and how to productively pursue my academic interests. Stephanie White charitably brought me into a real neuroscience lab as a research assistant when I, on paper, had no business being there. John Allman took my ideas seriously and guided me, with expert care, toward the better ones and away from the bad ones.

I have had a great experience working with my graduate advisors, Russ Fernald and Hunter Fraser. Both are wonderful advocates, collaborators, and mentors, and both have made possible whatever success I’ve achieved at Stanford.

Can you speak a bit to the role you see CEHG playing on Stanford campus?

I have found that CEHG provides a home for researchers who may be considered outliers or misfits in their own fields, be it due to their interdisciplinary focus or constant concern for achieving the next big thing (rather than what is currently fashionable). CEHG allows scientists to pursue these ideas at all levels – graduate, postdoc, faculty – knowing that they are supported both institutionally and intellectually.

As both a CEHG fellowship and research grant recipient, this has been really important for my growth as a researcher, and has allowed me to collect data and, in turn, produce work that is much more interdisciplinary and wide reaching than would have otherwise been possible.

What are your future plans? Where do you see yourself professionally in the next 5 or 10 years?

I am very excited to keep helping pioneer the study of behavioral evolution within the biological sciences. There is currently a small, but very motivated community of researchers who are working on ways to tackle this problem, and I would very much like to play a role in expanding this field’s focus and participation. To that end, I’m starting a postdoc this Fall in Tom Clandinin’s lab, to work on fundamental issues in the behavioral evolution of fruit fly species, and develop tools and methods that can be applied to a variety of species. In the future, I’d like to have my own lab, teach, and advocate for the benefit of using evolutionary perspectives in neuroscience, psychiatry, and human genetics.

What advice would you offer to other grad students or postdocs who are considering pursuing a similar educational and career path as you?

GET INTERESTED. It’s true that science is difficult, and to do it well requires knowledge of, and training in, an array of topics. But, in my experience, one of the main determinants of whether or not someone sticks with, and is successful in, science is their level of engagement with their topic.

Research benefits from an almost obsessive focus. Deeply wanting to know the answers to your questions somewhat forces the attainment of needed skills and knowledge. To me, this should be the way a researcher progresses, in the service of a project or question they are interested in, rather than in the service of the requirements of a graduate program or CV.

Tell us what you do when you aren’t working on research and why. Do you have hobbies? Special talents? Other passions besides science? 

I still compose, record, and perform music, though the amount depends on where my research is at any given moment. These days, I am increasingly interested in working on ways to integrate science and art, both in the production of my music and visual art, and in the way my scientific work is displayed and disseminated. I also rock climb quite a bit and am, as of recently, an extremely amateur dumpling maker.

 

Fellows Feature: Tricia Deng

Tricia Deng_ForWeb

Tricia Deng is a CEHG graduate student fellow in Dr. Jin Billy Li’s lab in the Genetics Department. She got her undergraduate degree in Molecular and Cell Biology (with emphasis on Biochemistry and Molecular Biology) at UC Berkeley. Her research focuses on the evolution and function of Adenosine-to-Inosine (A-to-I) RNA editing in Drosophila

Can you tell us a bit about yourself, personally and professionally?

I’m a graduate student in Jin Billy Li’s lab in the Genetics Department. I grew up in the South Bay. I went to UC Berkeley for my undergraduate degree in Molecular and Cell Biology. After graduating, I came to Stanford through the Structural Biology program. Then, I joined Jin Billy Li’s lab, which studies A-to-I RNA editing, and the Genetics program. I enjoy combining ideas and techniques from different fields of study. I think applying computational methods to biological research will dramatically improve the pace of research and yield exciting discoveries and innovations.

What initially got you interested in genetics and science?

I became interested in scientific research when I interned at an atmospheric chemistry lab at NASA in high school. I was really excited to be part of the research process and loved the idea that research could be used to address major challenges, such as global warming. I wasn’t very interested in biology until I worked on a research project in my senior year of high school and realized that biology research was very different from biology class, which was focused on memorization. In college, I really enjoyed learning about, and conducting, research through various classes and research projects led by some very talented professors and mentors, and this led me to pursue a PhD.

Can you tell us about your current research and what you want to achieve with it?

The information encoded in DNA is used to form the proteins that make up organisms; thus, this information contributes to various characteristics of organisms, including humans. Understanding this process is important for treating diseases, understanding how and why individuals differ, and improving the quality of life.

The process by which genomic information is used to make an organism is very complex. Many important modifications are made to the information before, during, and after transcription and translation. I’m studying one of these modifications, adenosine-to-inosine (A-to-I) RNA editing, which is important for neurological and immune well-being. In A-to-I RNA editing, enzymes in the Adar protein family convert adenosines to inosines at specific sites in RNA transcripts. These A-to-I changes can affect the amino acid sequence of the resulting protein, splicing, and the structure of the RNA. The fraction of adenosines that are converted to inosines at a specific site, or the “editing level”, can vary in different tissues and across developmental stages and times of day. Thus, RNA editing is different from SNPs, which work at the DNA level, and could be used to fine-tune the information encoded genomically.

Although RNA editing occurs at thousands of sites across the genomes of various animals, the functions of nearly all editing events haven’t been studied. Along with a former postdoc in the lab, Rui Zhang, I examined the evolution of A-to-I RNA editing in Drosophila species to identify editing events that are under evolutionary constraint and therefore likely to be functionally important. Then, working with some undergraduate and high school students, I used the Cas9/CRISPR system to make fly mutants without editing at some of these sites, and we’re working with other labs to examine their phenotypes. Finally, to study how particular adenosines might be selected to be edited, we used machine learning to examine how changes to the sequence and secondary RNA structure around editing sites are associated with changes in editing levels.

Overall, I think there are many open areas of research in this field. A better understanding of how RNA editing works and what its functions are – especially the functions of noncoding RNA editing events, which are understudied – will yield important insights into how our DNA information is used to produce phenotypes, and perhaps even give us clues for how complex systems, such as the brain, work.

Were there people to whom you would attribute your academic and professional success?

Before arriving at Stanford, I was fortunate to be mentored by many amazing researchers and teachers. At Stanford, my advisor, my lab mates, and other collaborators have been indispensable. I wouldn’t have been able to do so much without their feedback and the collaborations with many lab members and interns. Also, the support of friends and family – especially, my husband Jinghao – has been essential.

Can you speak a bit to the role you see CEHG playing on Stanford campus?

When I went to my first CEHG meeting, I was amazed at the diversity of research fields and departments there. I think one of CEHG’s strongest points is the ability to connect people from various fields. Many programs and events are focused on specific departments, but CEHG is different because it encourages the flow of ideas and collaborations between these fields.

What are your future plans? Where do you see yourself professionally in the next 5 or 10 years?

After graduate school, I plan to work in industry on something that will impact the world more directly. My future plans are flexible, but, no matter what I do, I hope to continue to work at the intersection of disciplines.

What advice would you offer to other grad students or postdocs who are considering pursuing a similar educational and career path as you?

I’ve realized that it helps to go to conferences and talk to people outside your field. Getting a PhD is often portrayed as specializing in only one thing, but, in reality, no area of biological research can be truly isolated into one field. Different fields can have different research priorities and approaches. Also, a lot of innovation comes from using new technology or pulling in outside ideas.

Also: Research is really hard, and you’ll likely face many setbacks, but you can do it!

Tell us what you do when you aren’t working on research and why. Do you have hobbies? Special talents? Other passions besides science?

I enjoy baking, eating, hiking, making apps and websites, and hanging out with my pet bunny, Momo. I also enjoy traveling and, especially, eating delicious food while traveling. My most recent trips were to Iceland (husky sledding on a glacier!) and China (giant mantis shrimps!). 

Fellows Feature: Amy Goldberg

Amy Goldberg_ForWeb

Amy Goldberg is a CEHG predoctoral fellow in the lab of Noah Rosenberg. Amy completed her B.S. in Biological Anthropology and Mathematics at the University of Michigan, where she was an undergraduate researcher in the lab. Her interests are in human evolutionary genetics, and she is currently working on mathematical modeling and statistical problems in anthropological genetics.

Can you tell us a bit about yourself, personally and professionally?

I grew up in Michigan, but was actually born in South Africa. I’m currently finishing my PhD in Noah Rosenberg’s lab. My background is in both anthropology and mathematics, and this combination continues to shape my research interests and how I address them. I develop quantitative methods to interpret genetic and archeological data to reconstruct past human demography, adaptation, and interactions with the environment. This work mixes population genetics with math and statistics, as well as biological anthropology, archeology, and paleontology.

What got you interested in genetics and science? Did you want to be a scientist as a child? 

My parents moved from South Africa to Michigan when I was young, and this degree is exactly what they had in mind. I’ve always liked science, but, as a kid, I thought that biology was mainly memorization. I’ll be graduating from the Biology department this year. This definitely shaped my view of education and how we talk to kids. Role models can be particularly helpful—we see a lot of occupations on TV or in movies, but scientist, especially professor, is vague. I had the opportunity to see my dad go to grad school; I went to his PhD defense when I was 12.

Can you tell us about your current research and what you want to achieve with it?

Much of my work focuses on human evolutionary history during the past 20,000 years, which is recent on evolutionary timescales. This time period is associated with massive social and environmental upheavals, from the end of the Last Glacial Maximum to worldwide megafaunal extinctions and the rise of agriculture. In fact, recent genomic studies have shown that this time period has been particularly important for shaping disease risk in humans because the history of recent expansions has led to a disproportionate number of rare genetic variants in the population. I build mathematical models to understand how evolutionary and social forces impact a population, and develop statistical methods to interpret large quantities of genetic and archeological data.

Most people I meet are innately interested in learning about human history, but this work has further consequences too, from predicting disease risk in diverse populations to forecasting the impact of climate change on animal populations.

What are your future plans? Where do you see yourself professionally in the next 5 or 10 years?

I am finishing my PhD this year. I’m excited to be starting my own lab at Duke, after deferring for a short postdoc at Berkeley. I plan to continue along major lines of research developed during my time at Stanford, and hope to keep in touch with many from the CEHG community. I’ll be tackling problems in evolutionary and population genetics, human-environment interaction, and recent population history.

Were there people (or one person) in particular to whom you would attribute your professional success? 

I’ve had a series of amazing mentors. Two in particular stand out—my undergraduate advisor Milford Wolpoff and my PhD advisor Noah Rosenberg.

I cannot discuss my scientific endeavors without thinking of my first scientific mentor, Milford Wolpoff. Before meeting Milford, I was hesitant to speak up for fear of being wrong; Milford taught me to be loud, to question what I read, and to know the history of scientific fields. It is also in Milford’s lab that someone casually mentioned an interesting geneticist on the other side of campus—Noah Rosenberg.

It is absolute luck that I met Noah mere weeks before he moved from the University of Michigan to Stanford. Since then, I have benefited in untold ways from Noah’s intentional efforts to include people from different backgrounds and instill thoughtful scientific habits. His encouragement—the simple belief that I could teach myself the skills I needed to know—underlies my whole PhD. The precision and skill with which Noah thinks is something I will continue to strive towards for the length of my career.

CEHG’s core values include “interdisciplinary research” and “collaboration.” Can you speak to the ways your work has embodied these values or to their importance to your future work or past experience? 

My work is really interdisciplinary and I’ve greatly benefited from CEHG bringing together scientists from across the university. I’ve learned from the professors, but also from the opportunity to interact with all the students and postdocs and the great speakers that visit for Evolgenome. More directly, CEHG sponsored my research through their grant mechanism for a project early in my PhD, which was the first collaborative project I participated in.

Tell us what you do when you aren’t working on research and why. Do you have hobbies? Special talents? Other passions besides science? 

Since my work is computational, I try to get outside for fun. Living in the Bay Area, that is easy. I go for a hike most weekends and have recently taken up climbing. I like to travel a lot too.

What advice would you offer to other grad students or postdocs who are considering pursuing a similar educational and career path as you? 

Figure out how to like to work early on—this will help you all other decisions like choosing mentors or to your field/subfield. Having a mix of people around with different personalities and research goals really helped me find my own way. I tried to frequently solicit their advice, but you don’t always have to take it. Outside the box opportunities are often overlooked but may be very worthwhile to starting a whole new line of research or to meeting collaborators.

 

Fellows Feature: Jaehee Kim

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Jaehee Kim is a postdoctoral scholar in the Department of Biology at Stanford University. She received her B.A. in Physics and Mathematics from Columbia University and her Ph.D. in Physics from Stanford University. Her research interests include mathematical properties of admixed population phylogenetic trees inferred by neighbor-joining, the relationship between individual identifiability and ancestry information in CODIS forensic markers and non-CODIS microsatellite loci, and change of admixture fraction in a hybrid population mating assortatively based on phenotype over time. 

Can you tell us a bit about yourself, personally and professionally? 

I was born and grew up in Incheon, South Korea’s third largest city, where I was likely the most physics-y kid on the block. True to form, I received a B.A. in Physics and Mathematics from Columbia University and a Ph.D. in Physics from Stanford University. My graduate research focused on the study of quantum chemical dynamics in complex molecules. I developed an ab initio theoretical framework to numerically simulate light-induced excited state topology and nonadiabatic dynamics, as well as multidimensional statistical techniques to analyze molecular fragmentation patterns. Now, I am a postdoctoral scholar in Noah Rosenberg’s lab.

How did you end up here? What got you interested in genetics and science?

Like most physics-y kids, I always loved math and spent countless hours voraciously reading science magazines and Feynman lectures. I was amazed by how physical phenomena, from mundane everyday events to the creation of the universe, could be explained by beautiful mathematical equations. I believed that everything could ultimately be explained by the laws of physics. During graduate training in atomic molecular optical (AMO) physics, working with people from diverse fields expanded my research interests. After going to a handful of outer department talks, I was drawn to evolutionary biology—like many people, I always have the same age-old questions lingering in the back in my mind: “why are we here; where are we going?” (Charles H. Townes, 1997). The current lab is the perfect fit for me as it applies rigorous mathematical theory and statistical methods to the study of human evolution and population genetics. I still have a lot to learn, but I have been enjoying working in the lab very much so far!

Can you tell us about your current research and what you want to achieve with it? 

My current research deals with the development and application of a mechanistic model for assessing the effect of different admixture histories involving dynamic contributions of mutually isolated source populations on the ancestry of admixed human populations. Human mating is non-random to some degree, since most people marry individuals of roughly similar phenotype and cultural factors. The assortative mating alters genetic variance for the assorting trait and makes the traits more susceptible to selection over time, thereby changing the genetic structure of a population.

Since the ancestry information is propagated through genotype but mating is based on phenotype, mapping genotype to phenotype is a crucial step. Among many interesting results the model produces, correlation between ancestry proportion and phenotype is of particular interest as it gives us insight about the degree to which genetic differences give rise to phenotypic differences between human groups. This also helps us to answer important questions regarding racial classification beyond conventional phenotypic group-level differences that are believed to be a representative of a race or ethnicity, for example, skin and eye color.

Once gaining intuition from the idealized model, to simulate more realistic human population, the model can be further extended by including confounding factors such as dominance, varying heritability, effect size distribution across loci contributing to the quantitative trait, and linkage disequilibrium, as well as environmental perturbations.

Were there people in particular to whom you would attribute your professional success? What is it like working with your current lab advisor and his lab? 

My Ph.D. advisor, Prof. Phil Bucksbaum, has provided me every bit of guidance for becoming a better scientist and encouraged me to collaborate with people outside the physics department to branch out into new research areas. His genuine enthusiasm for science and encouragement kept me motivated when research progress was bumpy. From my graduate lab, Doug taught me the importance of scientific intuition over sets of equations and he has made working in the lab so much more fun and interesting. James showed me reasonable science could be extracted from suboptimal experimental data if you used good statistical methods.

My current advisor, Prof. Noah Rosenberg, believes in the interdisciplinary nature of the work and gave me a chance to work in his lab. He helped me transition smoothly into the new field by providing every possible resource, and guided me through the systematic and mathematical approach for understanding evolutionary biology. I have also enjoyed the camaraderie and benefited from the varied expertise of the group members.

What are your future plans? Where do you see yourself professionally in the next 5 or 10 years?

Long term, I see myself still working in the field of theoretical population genetics. Having my own lab and staying in academia will be the best-case scenario, but I would be happy with government labs or industry as long as I can do meaningful research with some freedom and independence.

What advice would you offer to other grad students or postdocs who are considering pursuing a similar educational and career path as you? 

  • Most physicists are proficient in math and programming, but still, the more the better.
  • Stay open-minded, look outside your department, and explore your options. There are tons of other interesting work going on that could use a physicist!
  • Have patience, and don’t rush. Research takes time, and some projects might not end up working out. Persistence is important, but at the same time, know when to stop and move on, and when to pause for now and come back later.
  • Have a life outside the lab, and cut yourself some slack. You’ll need it for your sanity.

Can you speak a bit to the role you see CEHG playing on Stanford campus?

I love the cross-disciplinary environment CEHG has created. It brings scholars from various fields, which encourages me to communicate with researchers outside my specific research area and broadens my knowledge. I believe the collaborative approach across different fields can produce creative solutions to challenging problems through a diverse array of tools.

For instance, during my graduate studies in physics, I have used techniques borrowed from biology—for example, genetic algorithm and spawning of wavepacket—in modeling complex molecular dynamics. I am excited to apply physics techniques to tackling fundamental problems in evolutionary biology and share my interests with others.

Tell us what you do when you aren’t working on research. Do you have hobbies? Special talents? Other passions besides science? 

I spend most of my free time training in the gym. I have played various sports growing up, but my current focus is in Olympic weightlifting. I also like trying out new fitness classes/workshops/gyms and enjoy reading sports science and physiology research articles.