Fellows Feature: Sur Herrera Paredes

428A2066_ForWebSur Herrera Paredes is a CEHG post-doctoral fellow in the lab of Hunter Fraser. He is a graduate of the University of North Carolina at Chapel Hill. His research focuses on understanding the genetic basis and evolutionary consequences of host-microbe interactions.

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

I was born and grew up in Merida, Yucatan, Mexico. I went to college at the Cuernavaca campus of the National Autonomous University of Mexico (UNAM), where I enrolled in the Genomics program. That program was one of the first in the world that attempted to integrate computational and quantitative skill with the biological sciences, and it emphasized direct research experience. At the time, I worked on bacteriophage genome analysis and I got generally interested in what genomics can tell us about interactions between organisms.

After graduating college, I came to the US to work in a lab studying the root microbiome at the University of North Carolina at Chapel Hill, and I ended up staying there for my PhD in Bioinformatics & Computational Biology. During my PhD, I continued to work on plant-microbe interactions in the root and rhizosphere, trying to understand both the host genetic elements that control root colonization by bacteria and the effect that bacterial strains and/or consortia have on plant phenotypes.

From my work on plant-microbe interactions, I got interested in evolutionary questions regarding microbial adaptation to the host. It was that interest which drove me to the Fraser lab at Stanford, where I currently work.

How did you first become interested in genetics and science? Did you always want to be a scientist?

I always was attracted to research. There are many academics in my family, all of them work in social sciences and the humanities. I grew up reading and listening to mostly discussions about philosophy, political science and literature. I think that growing in that environment taught me how to approach and dissect complex problems where the unknowns greatly outnumber the certainties we may have. It also taught me to always question those certainties.

I probably would have been a social scientist, but, when I was twelve, I read Darwin’s autobiography, and when I was thirteen, I learned about Mendel’s experiments at school. I was fascinated by the fact that so many aspects of biology could be explained by so few and simple principles, but what really surprised me was that both scientists achieved their contribution through completely different approaches: Darwin through observation, and Mendel through experimentation.

I wanted to study genetics since then, and I was very lucky that UNAM created a genomics undergraduate program as I was starting high school. I really didn’t understand the difference between genetics and genomics at the time; I probably just thought they sounded similar, but as it turned out, it was one of the best decisions I have made since the UNAM’s program put me in direct contact with the bleeding edge of modern biological research, which led me to pursue a PhD and ultimately to my current work at Stanford.

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

In general, I am interested in biological mechanisms that link processes happening at multiple scales. As such, I find that inter-kingdom interactions are a unique opportunity to integrate the study of molecular processes with their implications for ecological and evolutionary scales. At the Fraser lab, I focus on characterizing the evolutionary processes that govern host-microbe interactions and microbe-microbe interactions within a host, and the role of these interactions on host health.

For one project, we are focusing on the role of microbial genetic variation within the human host. While the abundance of bacterial species and genes has been extensively studied in the human host, little is known about the evolutionary forces that shape bacterial genomes within hosts. I am leveraging bacterial genetic variation, inferred from metagenomic sequence data, in order to identify bacterial genes and pathways that are under positive selection in the human host. Furthermore, we want to know how bacterial genetic variants influence host health.

Besides bacteria, the human microbiome also includes microbes from other kingdoms (archaea and fungi). Specifically, bacteria-fungi interactions are relevant in the context of opportunistic infections, but almost nothing is known regarding bacteria-fungi communication and interaction among commensals in the human microbiota. Using yeast as a model, and a method developed at the Fraser lab that allows for high-throughput massive-parallel precision genome editing, I am investigating how yeast genetic variants associated with the human host influence the interaction of yeast with the bacterial human microbiota. Our goal is to identify novel genetic components of the molecular communication between yeast and bacteria, and to characterize the evolutionary forces that shape the evolution of those interactions.

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

Many people have have been essential for my professional success. It would be impossible to name them all, but I think that my family and their support has been essential. Also, all my lab mates, co-authors and collaborators have enriched my academic performance. And finally, my mentors over the years: Guillermo Dávila Ramos, my undergraduate mentor who let me work on a project I proposed, and that he knew nothing about; Jeff Dangl and Corbin Jones, my PhD co-advisors, who continuously pushed me to do the best science possible; and Hunter Fraser, my post-doctoral mentor for the last year, who has supported me in what is a novel direction for his lab.

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

I think that the most important things are that you enjoy what you do, and that you find people that you enjoy working with. There are many possible paths to achieving whatever goals, so one has to be open minded and work hard to achieve those goals, and working hard is much easier if you are having a good time.

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

I am influenced by my family of academics, but I see myself staying in academia and performing basic research for a long time. I would like to lead my own independent research group in a university setting that gives me the opportunity to participate in the training of the next generation of scientists. I would like to be in a place where there is high potential for many cross-disciplinary interactions, and with a strong commitment to basic research and cultural diversity.

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

I think CEHG is a fantastic organization for Stanford. One of the challenges at a big university is how to ensure that there is a forum to create synergistic interactions between different research groups. I think CEHG fulfills that role and it further helps to foster interaction between junior and senior researchers.

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

My hobbies have changed over the years. Since I did my PhD in a “plant lab,” I have been trying to learn how to germinate different types of plants. I enjoy literature; recently I have been focusing on Latin American literature, and English classics. I also like reading philosophy. I also enjoy biking and am learning how to fix my bike myself. I used to play a lot of chess when I was a kid; I left it for years but, thanks to two lab mates, I’m picking it up again.

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Fellows Feature: Rohan Mehta

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Rohan Mehta is a CEHG graduate fellow in Noah Rosenberg’s Lab. He is a graduate of the University of California, San Diego. His research is focused on theoretical population genetics, with a specific interest in the effect of evolutionary processes on the genealogies of genes.

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

I was born in Rochester, New York, but my family moved to southern California after a year and I grew up in Irvine. I went to college at the University of California, San Diego, so I have spent the vast majority of my life in California. At UCSD, I majored in both biology and mathematics and worked in a few different labs in the biology department. I am now finishing up my PhD in Noah Rosenberg’s lab here at Stanford, working on problems in theoretical population genetics.

How did you end up here? How did you first become interested in genetics and science?

I decided that I wanted to be a scientist from a very early age, though the specific kind of scientist changed a lot over the years. I’d always check out the same few books from the local library: a book on astronomy (I loved the renderings of stars); a book on chemistry (I loved the renderings of salts and crystals); and a book on fossils (I loved the renderings of ancient ecological communities). These books turned out to be quite prescient, as I started out wanting to be an astronomer, then a chemist, then finally a biologist.

The particular part of me that made me want to be a scientist was the part that was totally in awe of how cool every little thing was, if you really think about it–from the amazing diversity of life to the constructive power of chemical reactions to the sheer vastness of space. This is the part of me that is also drawn towards mathematics; there are underlying patterns and structures in everything, and all we need to do is find them.

I appear to have parked my drive to understand the phenomena of the natural world in the field of biology, specifically in the study of evolution. I am drawn to evolution because it is the fundamental process behind all of biology and because it is the key to understanding the patterns that we see in living systems. And if evolution is the key, then, for me, at least right now, that key is made out of population genetics.

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

My research is in the field of population genetics, focusing on an approach to studying the process of biological evolution and analyzing the genetic variation of a population and how that variation changes as a result of the forces of evolution. Most of my research has focused on the topic of gene genealogies: the ancestor-descendant relationships between individual genes. Every copy of a gene that you have is descended from some copy of that gene in your parents, and it turns out that the relationships between the individual genes in many people follow some very predictable patterns that we can use to try to figure out what happened to a population in the past. My goal for this line of research is to try to develop ways to study the histories of populations in terms of their size, ancestral relationships, and any migration that may have occurred between them.

I have also studied the mathematical properties of a common statistic used in population genetics to study population subdivision. I have found that this statistic has some interesting properties that must be kept in mind in order to properly interpret it. This statistic is very popular and is often mis- or over-interpreted, and if I can help people use it better then I will be a happy person.

Finally, I am currently working on studying anti-vaccination sentiment as what one might call a “cultural pathogen”, some sort of human behavioral trait that can be transmitted from person to person and that has a detrimental effect on some health-related trait (in this case, by hindering the acquisition of immunity towards a vaccine-preventable disease). I have found that transmissible anti-vaccine sentiment can change the dynamics of a disease in dramatic ways, making it much more difficult to get rid of the disease in a population. You can’t prevent disease transmission without properly understanding the relevant aspects of human behavior, and my work is intended to shed some light on the relationship between human behavior and disease.

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

I’d like to give a shout-out to my high school AP Biology teacher, Bruno Dworzak. I wasn’t really interested in biology until I took his class, and I acquired my love for evolution from him.

This would also be a good opportunity for me to thank my advisor, Noah Rosenberg, and the members of the Rosenberg lab. Working in the Rosenberg lab has been an excellent experience; it is a very friendly, supportive environment. Noah himself is an exceptional advisor who has really helped me guide my way through the often very muddy waters of the PhD process.

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

Find something that interests you on a deep level so that you want to stick with it through the rougher times, when you aren’t making much ostensible progress. I have had several occasions where it took me months to figure something out, and I’m not even doing experiments!

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

I plan to continue to use mathematics to study the process of evolution from a population genetics perspective, ideally leading my own research lab. I strongly believe in the importance of teaching and mentoring, so I plan to keep both as strong elements in my future plans.

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

CEHG’s Evolgenome seminars are a great way to bring together like-minded people who enjoy discussing interesting research in the fields of evolutionary and human genomics and I have learned a lot from the various talks given in this seminar series. The yearly symposium is also a notable event for bringing people from all over the place together to talk about their research. The fellowships offered by CEHG enable people like myself to conduct research that bridges the gap between fields (in my case, mathematics and evolutionary biology) in order to better understand nature and history.

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

My entire life outside of the lab is consumed by baseball: watching baseball, reading about baseball, competing in simulated baseball leagues with other people online, analyzing baseball statistics. Just all baseball. It’s a great way for me to take my mind off the never-ending turmoil of existence.

CEHG18 Event Report

This year’s Annual CEHG Symposium (a.k.a CEHG18) took place Monday, February 26, 2018 in Paul Brest Hall on Stanford campus.

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CEHG18 Audience, Courtesy of Saul Bromberger & Sandra Hoover Photography

The central purpose of this event was, first and foremost, to showcase the amazing research being done in CEHG faculty member labs. As CEHG’s faculty membership continues to grow (we are now home to 43 member labs from disciplines across the Humanities and Sciences and School of Medicine!), our academic community becomes even more diverse and impactful. This year’s speaker presentations truly embodied CEHG’s interdisciplinary and collaborative spirit.

Secondly, this year’s symposium featured keynote and guest speakers from the San Francisco Bay Area and beyond, representing CEHG’s consistent efforts to reach out into the larger scientific community and enable new conversations and collaborations that will inform and drive current and future CEHG projects.

Speakers

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Keynote Anne Stone, courtesy of Saul Bromberger & Sandra Hoover Photography

This year’s keynote presenter, Dr. Anne Stone, traveled from her home institution, Arizona State University (ASU), in order to enlighten us on “The Origins and Evolution of Tuberculosis in the Americas.” As Principal Investigator (P.I.) of ASU’s Stone Lab, Dr. Stone is an expert in the field of anthropological genetics, making her the perfect headliner for CEHG’s annual flagship event; her research, as well as the work currently being conducted in her group, is essentially cross-disciplinary, variously involving bioarchaeological, molecular genetic, population genetic, and genomic analyses.

Guest speakers were nominated by various members of the Executive Committee, thereby representing our faculty’s varied disciplinary interests and expertise. Dr. Graham Coop–currently Professor of Evolution and Ecology at the University of California, Davis and formerly a postdoctoral scholar in CEHG Director Jonathan Pritchard’s group in the Department of Human Genetics at the University of Chicago–presented on his work at the intersections of population biology and quantitative genetics.

Dr. Lauren O’Connell, new Assistant Professor in Stanford’s Biology Department and PI of the O’Connell Lab, shared some findings from her current work on “Chemical Ecology in Poison Frogs.” Her lab uses amphibians as a model system for understanding the molecular and genomic contributions to biological diversity, as they display tremendous variation in behavior and physiology.

Assistant Professor of Statistics and of Biomedical Data Science at Stanford, Dr. Julia Palacios explored scientific responses to the important question, “How Much History Can We Learn from Genetic Data?” As P.I. of the Palacios Group, her core research interests include developing and using statistical methods to understand observed genetic variation in humans and pathogens. Her presentation was informed by her work in efficient statistical inference and efficient probabilistic modeling in evolutionary genomics, infectious diseases, and more general stochastic processes that could have significant impacts on public health.

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Guest Speaker Dr. Pleuni Pennings, Courtesy of Saul Bromberger & Sandra Hoover Photography

Our last speaker of the day, Dr. Pleuni Pennings (currently Assistant Professor in San Francisco State University’s Department of Biology), has a long-standing working relationship with Stanford CEHG; she formerly served as CEHG’s Communications Manager and was a postdoctoral scholar in CEHG Executive Committee Member Dmitri Petrov’s Lab. It was wonderful to see her again and to hear her speak about her current research on “The Evolution of HIV Evolution.” Click here to read more about the HIV research currently being conducted in Dr. Plenning’s CODE Lab.

Our trainee speakers were truly impressive in the breadth of their research interests and their passionate scientific engagement. Current and previous Stanford CEHG Fellow speakers included Arbel Harpak (from Stanford’s Pritchard Lab), Chao Jiang (Snyder Lab), and Gili Greenbaum (Rosenberg Lab). More CEHG trainee member research was showcased in presentations by Emily Ebel (from Stanford’s Petrov Lab), Peyton Greenside (Kundaje Lab), and Eilon Sharon (Stanford Fraser and Pritchard Labs). As a special guest in CEHG Director Marcus Feldman’s Stanford lab, Martin Pontz (from the University of Vienna) presented his graduate work, located at the intersections of mathematics and biological science, on “Deterministic and Stochastic Two-Locus Models.”

Registration and Attendance

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CEHG18 House, Courtesy of Saul Bromberger & Sandra Hoover Photography

More than 160 students, faculty, University staff, and industry affiliates registered for this year’s symposium, and 130+ attended speaker sessions, the keynote presentation, lunch, and poster presentations, indicating substantial interest in the work our faculty and trainee members are doing in their respective CEHG labs, and active engagement amongst our community members.

We were also thrilled to see, and catch up on the exciting work of, friends and colleagues from the National Autonomous University of Mexico (UNAM) and LANGEBIO Mexico who attended this event. CEHG co-sponsored this year’s Tinker Symposium on Latin American Research for Biodiversity, which took place in the two days following the CEHG18 Symposium. Many UNAM and LANGEBIO Mexico attendees arrived in the US early, specifically for the purpose of attending our CEHG18 Symposium. Their presence was truly appreciated, and contributed significantly to the high quality of event interactions and post-presentation discussions.

Lunch and coffee breaks made this event an important networking opportunity for our (junior and senior) community members and visiting scholars. Event photographs display the joy CEHG members experience in connecting with one another–reuniting with long-time colleagues and collaborators, making new academic friends and partnerships, and (re)connecting with faculty and trainees from other labs and academic institutions.

Venue/ Vendors

We have held previous Center events at Paul Brest Hall (located in Munger Complex), and over time have come to view this venue as symposia home base. It is just the right size for our 130+ event size, lighting is warm and comfortable, facilities are clean and new, and Munger staff are always attentive, responsive, and courteous.  AV staff manage presenter slides and resolve technical problems, making event facilitation that much easier for staff.

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CEHG18 Attendee, Courtesy of Saul Bromberger & Sandra Hoover Photography

For event photography, we have worked for the last three symposia with Saul Bromberger from Saul Bromberger & Sandra Hoover Photography. Saul is always a pleasure to work with, and his photographs capture the energy and intense engagement of speakers and audience members alike. If you would like to see photos from CEHG18 (and other Center event and program albums), click here.

Volunteers

This event would certainly not be possible without the active engagement and dedicated service of our trainee volunteers. It takes more than a dozen volunteers to facilitate an event of this size, and our trainee volunteers were involved with every level of event operations. Volunteers (namely, Ziyue Gao, Jing He, and Chuan Li) emceed our speaker sessions, introducing speakers, facilitating Q&A sessions, and keeping track of presentation times. Mic runners included current CEHG Fellows Arbel Harpak and Boxiang Liu, and visiting UNAM scholar, Miriam Bravo.

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Volunteer Emcee and Current CEHG Fellow, Chuan Li, Courtesy of Saul Bromberger & Sandra Hoover Photography

Designated volunteer tweeters–including Sur Herrera Paredes, Yuping Li, and Arturo Lopez Pineda–covered all of our CEHG18 speaker presentations (search #CEHG18 on twitter to catch up on their thread). Arturo also helped run our registration table, along with CEHG trainee members, Karthik Jagadeesh and Aashish Jha. Last, but certainly not least, CEHG volunteers Ziyue Gao and Laksshman Sundaram supported staff during setup and clean-up pre- and post- event, along with visiting UNAM scholar, Viridiana Villa Islas.

As you can see, it takes a village to run a large academic event like the annual CEHG symposium, and our village is comprised of extraordinarily committed, selfless, service-minded pre- and post-doctoral trainees. We would be truly remiss if we did not take this opportunity to thank our volunteers for their time, talents, and continuing commitment to making CEHG a remarkable place to work, learn, and grow.

More Appreciation

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CEHG Co-Directors, Drs Marcus Feldman (left) and Jonathan Pritchard, Courtesy of Saul Bromberger & Sandra Hoover Photography

CEHG staff would like to take this final opportunity to thank our Directors, Drs. Marcus Feldman and Jonathan Pritchard, and our Executive Committee–comprised of Drs. Carlos Bustamante, Hank Greely, Dmitri Petrov, Noah Rosenberg, and Chiara Sabatti–for their vision, guidance, and support throughout the CEHG18 planning process.

CEHG19 

Center staff are already in the process of planning next year’s annual symposium (a.k.a CEHG19). To stay abreast of event news and receive symposium updates as soon as they are available, contact us at stanfordcehg@stanford.edu; ask to join our Stanford CEHGCenterall listserve. We hope to see you at CEHG19!

Fellows Feature: Megan Morikawa

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Megan Morikawa is a postdoctoral scholar at UCSB and a marine researcher with the Iberostar Hotels and Resorts. She is based in the Dominican Republic, working with the private sector to conduct research on coral restoration in the Caribbean. She received her PhD in 2018 at the Palumbi Lab at the Stanford Hopkins Marine Station in Monterey. In her PhD, she conducted research on multi-species coral nurseries see if coral reef restoration can be made ready for climate change using genomic tools to unveil natural diversity in reefs in the Pacific. She also studied the impacts of seasonal shifts in coral transcriptomes on the response during bleaching stress. She was a Robertson Scholar at Duke University before her time at Stanford.

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

My name is Megan Morikawa, I just graduated from the PhD program at Stanford’s Marine Station in Monterey, and I’m working to understand how coral reefs can survive a changing climate. I’m dedicated to working at the intersection between research (specifically conservation genetics) and application (specifically marine conservation), and am recently excited about the ways private industry and private philanthropic funding can reward risk taking in pursuing research in this intersection.

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Photo courtesy of Megan Morikawa. 

I graduated from Duke University in 2012 with a personalized major titled Conservation Biology and Genetics: Applied Environmental Sciences. I did my PhD on understanding the role variability (across seasons, individuals, and species) played in restoring coral reefs that were more resilient to bleaching events. I’m now living in the Dominican Republic, working with a Hotel called Iberostar and as a postdoc at UCSB to test the feasibility of multi-species, climate resilient coral nurseries in the Caribbean.

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

My father is an engineer and my mother is an artist. In many ways, I am very much a mixture of the two. I’m passionate about the science that provides a technical solution to a real world problem. I’m also passionate about communicating that research in creative ways and thinking creatively about solutions and applications.

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

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Photo courtesy of Megan Morikawa. 

Coral reefs are facing widespread and recurrent global bleaching. This jeopardizes a critical resource that not only provides astonishing ecosystem services, but makes the world worth protecting. With ocean warming, sea waters can raise by a few degrees, particularly during El Niño years. While a few degrees may not seem like a large perturbation, it can cause the breakdown of symbiosis between animal coral host and algae obligate symbiont, also known as bleaching. The coral expels damaged symbionts, thus revealing the white skeleton beneath their otherwise clear tissue and removing their major food source. This often leads to coral death.

Research on the specific biology of this symbiosis has shown that not all bleaching is the same and that some species and some individuals are more resilient to bleaching than others. My PhD research had three parts: 1) comparing bleaching across species by characterizing shared transcriptomic response to acute heat stress; 2) understanding how variability in thermal tolerance within species could be used to restore reefs more resilient to climate change; and 3) scaling the practice of finding resilient coral to a country scale.

The research has allowed for exciting opportunities to work with management partners in American Samoa and Palau to integrate an understanding of thermal tolerance and reef restoration in their management initiatives. It also led to some great opportunities for outreach to a broader public about why research like this matters to coral reefs (check out the HHMI video with my advisor Steve Palumbi). Finally, it has opened doors to engage with the private sector on ways to integrate conservation initiatives into their business practice, which is a major part of the job I have currently!

Were there people in particular to whom you would attribute your professional success?

I was so fortunate to have a high school mentor who changed my life track forever. Dr. Jay Vavra at High Tech High was the first to introduce me to genetics, started a project to test the feasibility of using DNA as a tool to identify mislabeled wildlife products in the bushmeat trade, which kickstarted my career in conservation genetics. From that point, there were a string of incredible mentors from a diverse set of fields that have brought me to where I am today. Jeanne Kirschner at the Roberstons Scholars Program so strongly believed in my unconventional journey, even when I did not. My undergrad mentor Hunt Willard welcomed and supported my interests even when they were far outside his expertise and taught me that we’re never too old to have mentors. And so many faculty at the Hopkins Marine Station have provided not only the intellectual but emotional support I see as critical to any student’s professional success.

Above all, my advisor, Steve Palumbi, has created a lab space where I could pursue ambitious projects, grow as an investigator, grow as a communicator, and test the waters as a project manager and mentor in the lab and in the field. A relationship with your PhD advisor is a long commitment, so I suggest that you find someone who compliments your own work style (do you like to have lots of freedom? Do you like to have structured deadlines? Do you work best under a bit of pressure?), someone who cares about your wellbeing (because that ultimately benefits their lab and their professional success!), and someone who does not shy away from setbacks (since there will always be challenges in the PhD!).

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

Research should not happen in isolation. Yet so often, we struggle to have conversations outside of our field. CEHG allows groups of networks to come together and have a great mix of comfortable conversations and conversations that push us (or at least me!) outside of our comfort zones. As a student at the Hopkins Marine Station, it was one of the only ways that I maintained a steady tie to main campus till the end of my graduate career. For that, I’m thankful for the opportunity to both share research on coral reefs but also gain knowledge about the frontiers of all members of CEHG.

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

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Photo courtesy of Julia Mason. 

I am currently working with the hotel company Iberostar and UCSB to conduct research on multi-species, climate-resilient nurseries in the Caribbean. We are also working on a larger initiative to promote sustainable practices within the company. Follow https://twitter.com/mkmorikawa to learn more about what we’re up to!

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

In my career, I’ve tried to maintain an applied focus to the research I’ve conducted. I could not encourage you more emphatically to keep pursuing applied research if you are considering the same. It has opened up incredible opportunities to work with different industries, and different perspectives that almost always improve your science (albeit in unexpected ways).

Advice to follow a similar path would be: 1) Work on skills outside of just producing good science, such as communication, managing a budget, mentoring, negotiations, non-traditional media, and more. 2) Expand upon the last paragraph you would write at the end of your discussion. In these sections, we often say “this research could be useful for x, y or z.” I encourage you to think about this at the start of the project, and see if there are easy conversations you can have at the beginning to make real world application more of a possibility from the beginning. 3) Treat every new contact as an exciting opportunity to learn about new fields & new applications (and potentially new collaborators!), particularly if they are outside of academia. Networking is not something that happens one time in a concentrated event. I think it’s best when it is a slow, gradual process that becomes more meaningful because of 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? 

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Photo courtesy of Megan Morikawa.

When I’m not working on research, I’ve got too many strange hobbies! I play the guitar & sing (a great artistic compliment to the more analytical side of research), I’m starting to learn woodworking (the latest project was a crazy end-grain cutting board), I play with microcontrollers like the Arduino (I suppose equally useful to sciences), I enjoy cooking and baking (usually inversely related with time in the lab – I’m currently into making pasta), I also have an ongoing project to make biologically accurate marine organisms as crocheted tree ornaments. I highly recommend using the incredible resources/studios/clubs Stanford has available to play around with new skills! 

Fellows Feature: Karthik Jagadeesh

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Karthik Jagadeesh is a CS Ph.D. student in the Bejerano Lab. He has a B.S. in EECS and B.A. in Applied Mathematics from UC Berkeley. He is building statistical models to identify disease causing mutations and computational tools to improve rare disease diagnosis.

Let’s start by having you to tell us a bit about yourself, personally and professionally. 

I am a Computer Science PhD student in Gill Bejerano’s research group. My research is focused on studying the human genome to build computational tools and statistical methods to better interpret patient’s genomes and diagnose Mendelian diseases. Prior to joining Stanford, I did not have much exposure to computational biology, but I fell in love with genomics after joining the Bejerano Lab and seeing how we can extract meaning from genomic code. I completed my undergraduate degree from UC Berkeley in EECS and Applied Math, where I had brief research stints in databases and computer security and completed an honors thesis exploring approximation algorithms in Applied Mathematics.

I grew up 20 minutes south of Stanford in Saratoga, CA and am a Bay Area native. I enjoy playing tennis, hiking, and traveling in my free time.

Why did you become a scientist? Did you want to be a scientist as a child?

I spent my childhood at the center of the internet technology revolution in Silicon Valley. Growing up in this environment, I was impressed by the impact people here had on the local community and the world. I soon realized that fundamental research in science and technology is what allows this impact to be possible. Starting in undergrad, I explored various research topics and was particularly excited by data and applied machine learning problems. After coming to Stanford, I found that computational tools have the ability to transform our understanding of the human genome. From the compilation of my undergrad research and work experiences, I have refined my interest in computational genomics and specifically human disease genomics.

Can you tell us about your current research and what you hope to achieve with it? You could start by listing 3 words you think best represent or embody your research.

Mendelian disease diagnosis.

My research goal is to bridge the gap between genotype and phenotype, and understand the ways in which genetic variation contributes to phenotypic diversity and ultimately human disease. Mendelian diseases are diseases that are caused by mutations to a single gene. As typical individuals have around 4 million variants genome wide, we aim to develop computational techniques to find that “needle in the haystack”. Using data from next-generation sequencing and tools from computational biology and machine learning, I have worked on projects ranging from machine learning for variant pathogenicity prediction to cryptographic techniques for genome privacy.

M-CAP, a machine learning classifier, reduces the variants of uncertain significance in patient genomes by 60% while maintaining high sensitivity, and has become widely incorporated into exome analysis projects and pipelines. The scores are available through the popular ANNOVAR tool as well as through dbNSFP. Additionally, thousands of users have downloaded our VCF file of exome wide scores and hundreds of users query our online web search tool every day.

Another recently published project on genome privacy introduces a secure framework to compute flexible functions over genomes from multiple individuals while preserving patient’s genomic privacy. Genome privacy is becoming more important, especially as we start to understand more about the genome and how it encodes function. It is critical to build secure methods for genomic analysis as this allows individuals to continue to share their genomes while maintaining anonymity.

Recent Press on genome privacy:

Were there people in particular to whom you would attribute your professional success?

There are many people that have helped me get to where I am and for whom I am deeply grateful, including my family, my lab mates and especially my mentor Aaron Wenger and my advisor Gill Bejerano.

Aaron taught me a lot about genomics, specifically in the context of disease, and he helped me frame my first project, and structure a concrete approach to tackle it. I have continued to employ a lot of these strategies I learned from him on projects I worked on later. Aaron and Harendra Guturu (another one of my mentors) both built many of the computational tools and data processing pipelines that are a foundation of the medical genetics work I have done.

Gill gave me an opportunity to join his lab though I came with no background in biology. One of my favorite parts about working with him is the interesting discussions and brainstorming sessions that we have. He constantly pushes me to think deeply about my research and asks questions, forcing me to have a thorough understanding of the underlying methods. Gill also has a detail-oriented approach to research, writing, and presenting which has taught me not only how to approach research but to also package and present my work so it can be understood by multiple audiences.

Research is a truly collaborative process and working with the members of the Bejerano lab and seeing how ideas and tools have been passed down and improved generation by generation has really influenced my experience as a PhD student.

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

I am planning to graduate in the summer and am currently applying to postdocs. I hope to continue improving our understanding of the genetic basis of diseases, specifically through expanding interpretability of the noncoding genome and complex diseases. Eventually, I hope to become a PI with a lab focused on developing computational methods to improve the understanding of the genetic architectures of human disease.

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

CEHG is awesome! CEHG organizes many interesting talks and lectures throughout the year, such as the CEHG symposium, and these events provide a great opportunity to learn about new topics as well as meet other people working on related topics.

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

In general, I feel there are a lot of interesting opportunities at the intersection of fields. As a young scientist, it is good to spend time developing a strong foundation and skills in two diverse areas. This allows you to have the expertise to build novel solutions to problems by connecting ideas from different areas – something not many can do.

 

 

Bridging cultural gaps: scholars promote interdisciplinary studies in human cultural evolution

Within the blink of an eye on a geological timescale, humans advanced from using basic stone tools to examining the rocks on Mars; however, our exact evolutionary path and the relative importance of genetic and cultural evolution remain a mystery. Our cultural capacities—to create new ideas, to communicate and learn from one another, and to form vast social networks—together make us uniquely human, but the origins, the mechanisms, and the evolutionary impact of these capacities remain unknown.

Evolutionary biology is at an exciting juncture. Much important research has focused on the human genome as the key to unlocking knowledge about our evolutionary history. Recently, however, researchers have begun to recognize that understanding non-genetic inheritance, including culture, ecology, the microbiome, and regulation of gene expression, is fundamental to fully comprehending evolution. The evolutionary effects of culture, learning, and language have generated heated and dynamic debate and new interdisciplinary studies of human evolution. Now more than ever it is important to focus on the dynamics of cultural inheritance at different temporal and spatial scales, to uncover the underlying mechanisms that drive these dynamics, and to shed light on their implications for our current theory of evolution as well as for our interpretation and predictions regarding human behavior.

Many academic disciplines study human behavior and culture—anthropology, biology, psychology, computer science, ecology, economics, cognitive science, and archaeology, to name a few—often using different vocabularies. Two Stanford researchers, postdoctoral fellow Oren Kolodny and Professor Marc Feldman along with former Stanford postdoc Nicole Creanza, thought that researchers in these different fields could learn from one another to shed new light on human cultural evolution.

Their efforts to promote interdisciplinary work in human cultural evolution has led to a new theme issue in the world’s oldest scientific journal, Philosophical Transactions of the Royal Society B. In this special issue, Kolodny, Creanza, and Feldman aimed to combine perspectives from diverse fields to help elucidate the cultural forces affecting human evolution. The outcome is an interdisciplinary collection of research on the roles that culture plays in shaping the course of human evolution, exploring the mechanisms of cultural evolution from their cognitive underpinnings in individuals, through the behavioral ecology of learning from others, to the dynamics of transmission at the level of individuals and populations.

The issue also includes individual contributions authored by Kolodny, Feldman, Creanza, and co-authors, on the evolution of the human capacity for language, on linguistic cultural origins of the Creole language Sranan, and on the links between heritability, genes, and culture.

The sixteen new scientific publications in this issue were shaped by an international workshop entitled “New Perspectives in Cultural Evolution,” held at Stanford University in July 2016, supported by the John Templeton Fund. This workshop brought together researchers from multiple fields from different universities. With special focus on open discussions in large and small groups, participants in the workshop proposed new ways to synthesize fields, tackled current controversies, and highlighted important unanswered questions, leading to the new research published in the theme issue.

This research was supported by the John Templeton Foundation and the Stanford University Center for Computational, Evolutionary, and Human Genomics.

MAIN ISSUE PAGE:

http://rstb.royalsocietypublishing.org/content/bridging-cultural-gaps-interdisciplinary-studies-human-cultural-evolution

Table of contents when it goes live:

http://rstb.royalsocietypublishing.org/content/373/1743

PAPERS:

Kolodny O, Feldman MW, Creanza N (2018). Bridging cultural gaps: the interdisciplinary nature of cultural evolution. In press. Philosophical Transactions of the Royal Society of London: 20170413.

Kolodny O, Feldman MW, Creanza N (2018). Integrative studies of cultural evolution: crossing disciplinary boundaries to produce new insights. In press. Philosophical Transactions of the Royal Society of London: 20170048.

Feldman MW, Ramachandran S (2018). Missing compared to what? Revisiting heritability, genes and culture. In press. Philosophical Transactions of the Royal Society of London: 20170064.

Kolodny O, Edelman S (2018). The evolution of the capacity for language: the ecological context and adaptive value of a process of cognitive hijacking. In press. Philosophical Transactions of the Royal Society of London: 20170052.

Sherriah AC, Devonish H, Thomas EAC, Creanza N (2018). Using features of a Creole language to reconstruct population history and cultural evolution: tracing the English origins of Sranan (2018). In press. Philosophical Transactions of the Royal Society of London: 20170055.

MEDIA CONTACTS: Oren Kolodny tel: 650-665-3296 email: okolodny@stanford.edu, Marcus Feldman tel: 650-725-1867; e-mail: mfeldman@stanford.edu

Department of Biology, Stanford University, Stanford, CA

Nicole Creanza tel: 407-252-8361 e-mail: nicole.creanza@vanderbilt.edu

Department of Biological Sciences, Vanderbilt University, Nashville, TN

Fellows Feature: Arbel Harpak

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Arbel Harpak is a CEHG graduate fellow in Jonathan Pritchard’s lab. He holds BSc degrees in Mathematics and Physics, and MS degrees in Biology and Statistics.  In his PhD research, Arbel asks how mutational mechanisms and natural selection shape genetic variation.

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

I grew up in Israel. My family moved around quite a bit, but always kept a stone’s throw away from the beaches of the Mediterranean Sea, where I spent a lot of my time. I was very much into math and into wildlife from a young age, but hadn’t really thought of being an academic; no one in my family was, and playing outside with a ball of some shape or form filled up most of my schedule nicely. I only started my B.Sc. at 23, after a long military service, a short stint in industry, and some travel in Asia. While it sometimes feels like a late start compared to my fellow grad students, I am happy to have these bits of life experience outside Academia.

 I started my bachelor studies in Mathematics and Philosophy at the Hebrew University of Jerusalem, and, later on, added Physics to the mix. I deeply enjoyed my Math studies. I never knew—and probably never would have known without my Math education—how it feels to fundamentally and thoroughly understand your object of study. This feeling was a source of real joy for me.

My first research experience was in studying bacterial colony growth dynamics with the Physicist Nathalie Balaban during undergrad. This exposure to Biological research led to my M.Sc. work with Guy Sella (now at Columbia University). In my Masters, I developed theoretical expectations for genetic diversity in evolutionary experiments with micro-organisms, and conducted an experiment in the Balaban lab that tested these expectations. During this time, I got to read lots of inspiring research coming out of Stanford Evolution and Genetics labs; this led me to apply to join Stanford Biology’s Eco/Evo track.

How did you first become interested in genetics and science?

My Masters was probably the first time I started to seriously think about a career in research, mostly thanks to Guy Sella, who made the introduction to Population Genetics extremely exciting. He helped me form a reading list, starting from popular science books about evolution (e.g. Charles Darwin, Sean Carroll, Jerry Coyne and Neil Shubin) advancing into the fundamentals of Population Genetics and Coalescent theory (e.g. John Gillespie, Dick Hudson, Allen Orr, R.A. Fisher, Simon Tavaré, Charlesworths) and eventually contemporary research papers. He encouraged me to spend my first 4-5 months only reading, simulating evolutionary dynamics and periodically updating him on what I learned. In these conversations, he always thoughtfully guided me, but also had genuine interest in my own (probably quite naïve, in retrospect) thoughts. For me, this was a great experience that filled me with excitement for Population Genetics research.

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

Most of my doctoral work has been the study of mutational mechanisms, and how they shape human genetic variation. For example, analyzing >120K human exomes in the ExAC dataset, I found that many positions in the human genome were segregating mutations of more than one independent origin. This revealed substantial mutation rate heterogeneity even within what is considered a single mutation type.

What I like most about this work is being able to use large genomic variation datasets and Statistics to make discoveries about basic genetic mechanisms. The extent of mutational heterogeneity can be hard to quantify in direct experiments because of their limited sample sizes—but these huge genetic variation datasets contain evidence from a very long experiment: our own evolution.

I also work on the evolution of gene families. I helped develop riboHMM, a method with which we identified thousands of novel coding sequences in the human genome—some of which had surprising functions. For example, some of the novel sequences function as a regulatory “sink” of gene expression: they occupy Ribosomes and thereby reduce the expression of other genes. In more recent work, I estimated the rate of genetic exchange between gene duplicates. This exchange is a driver of >20 diseases and is also thought to be a central force behind the “concerted evolution” of gene duplicates—a curiously low level of divergence between duplicate genes that is sometimes observed long after their duplication.

What kind of responses have you gotten to your research/findings?

People are often excited to hear about my NYC rats research. This is a collaboration with Pleuni Pennings, Nandita Garud, Noah Rosenberg, Dmitri Petrov and Jason Munshi-South. New Yorkers (and people of other cities of course) are vividly aware that rats have adapted to urban environments impressively; we wanted to know whether this adaptation has a genetic basis. We have collected rats from abandoned lots around New York City and are scanning their genomes for unusual signs of adaptation. I love talking to people about this research because it illustrates evolution beautifully in comprehensible timescales, and with natural phenomena that one can see even in the most urban setting.

What happens next in the process of discovery?

Lately, my work has focused on highly-polygenic (“complex”) traits. Although most diseases and other traits are polygenic—i.e. affected by many different sites in the genome—most of our contemporary models and tools are best-fitted for a Mendelian world. Together, with lab mates who have already made significant discoveries in this area—Yair Field, Nasa Sinott-Armstrong and Evan Boyle—we are analyzing genome-wide association studies (GWAS) to learn about the genetic architecture of polygenic traits, and study this architecture’s implications on human evolution.

Are you enjoying your time at Stanford? 

Stanford is like Disneyland for academics. I can’t think of anywhere else I’d rather be for my Ph.D.

What is it like working with your current lab advisor and his lab?

More than anyone, my advisor, Jonathan Pritchard, is the person that shaped me as a scientist and has been a role model for me. He is a man of few, selected words who usually teaches by example: he is nearly always the quickest to identify the right questions to ask and the first to make sharp inferences. He strikes a balance between being constantly productive and engaged in everyone’s projects, and still managing to come up with innovations completely out of left field. I think a big part of this is his habit of occasionally zooming out—and taking the time to truly think and rethink about data critically.

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

Outside of research, I learnt everything I know from Tami and Eric Taylor.

Professionally? that’s such a long list. I am grateful to Stanford faculty that help with key advice along the way, notably Noah Rosenberg, Dmitri Petrov, Christina Curtis, Hunter Fraser and Marc Feldman.

Another large group that I owe a debt of gratitude to are my past and present fellow lab members. Just to give a few examples: I learned what true scholarship looks like from Ziyue Gao, Eilon Sharon, Jamie Blundell and Alison Feder; how to allow data to whisper secrets in your ear from Evan Boyle, Kelley Harris and Eyal Elyashiv; how high productivity and always making yourself available to help others can go hand in hand from Pleuni Pennings, Anand Bhaskar and Nasa Sinott-Armstrong; how to do statistical modelling that is revealing rather than hiding the signal in the data from David Golan, Anil Raj and Doc Edge; how to effectively communicate science from Emily Glassberg, Harold Pimental and Yang Li; this list goes much longer—but I should probably spare CEHG blog readers at this point.

Where do you see yourself professionally in the next 5 or 10 years?

I aspire to start my own research group and combine research with teaching. I would like to lead a group that investigates a biological question with whatever means necessary—a lab that is not too comfortable in its comfort zone. I am also quite passionate about teaching. I got to work as a high-school and college Math teacher to fund myself through my B.Sc. studies, and found it to be highly fulfilling. While I truly enjoy the footwork of applying statistical analysis to questions in Genetics and Evolution, I believe that the greatest impact I could have on the field is in teaching, advising and mentoring future generations; that is just how exponential functions work.

As a CEHG fellow, can you speak a bit to the role you see CEHG playing on Stanford campus?

I am proud to be a part of the CEHG community. CEHG brings together labs with shared interests from many departments at Stanford. Evolgenome seminars provide exposure to cool work and encourage interdisciplinary connections. I am particularly grateful for the generous CEHG fellowship—it allowed me to pursue my deep interest in the adaptation to urban environments in NYC rats and in polygenic trait evolution during the last year of my Ph.D.

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? How do these values align with your own approach to science?

In CEHG symposium 2016, I got to hear a talk by Christina Curtis and ask her many questions about it after. This conversation boosted a new research direction for me, and ignited brainstorming meetings with Christina Curtis and Zheng Hu and Ruping Sun from her cancer genomics lab. These meetings naturally developed into a collaboration with the Curtis lab in applying Population Genetics to better understand tumor progression. I feel quite fortunate to have been at the right place and time (= CEHG symposium 2016) that made this interdisciplinary connection possible.

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

If I had to identify one necessary but not sufficient condition for success in grad school, it is being excited about your research. It doesn’t have to be the research question; it could be the method or the people that you get to work with. Academic research careers can be very unrewarding externally, so if you are not internally fueled, grad-school crises might last years instead of weeks.

Other than that, I think it’s important to set high standards for yourself in what you want to excel at. For me, often times this means doing things painfully slowly—but from scratch and by myself.

Lastly, let me also confuse you with some contradictory-sounding piece of advice: get the most out of your colleagues’ experience, and give back as often as you can. I have personally learned that having science buddies—or better yet, science BFFs—is the single strongest determinant of my happiness in my work.