Category: Students Page 30 of 42

Students Brief Senate, FDA, & Personalized Medicine Coalition

On April 13, 2015

In Biology, Cancer, Genetics/Genomics, Students

By Nonie Arora

Duke students and faculty brief Senate staffers, Pictured left to right: Allison Dorogi, Nonie Arora, Robert Cook-Deegan, Samantha Phillips, Jenny Zhao, Elisa Berson. Credit: Robert Cook-Deegan

The week of April 13, at the height of cherry blossom season, Duke students traveled to Washington, D.C. to brief senior staff members of the Senate, Food and Drug Administration (FDA), and the Personalized Medicine Coalition (PMC). Over the spring semester, five students in the Genome Sciences & Policy Capstone course (including myself) studied the regulatory framework of laboratory developed tests (LDTs).

LDTs are tests developed for use in a single laboratory. The clinical laboratories that develop LDTs are considered to be medical device manufacturers and are therefore subject to FDA jurisdiction. The FDA exercises “enforcement discretion” over LDTs, which means they choose when to regulate these tests.

Duke students in Washington, D.C. Credit: Robert Cook-Deegan

Under the supervision of Duke professor Robert Cook-Deegan, we dove into five case studies regarding different types of LDT tests.

The case study that I focused on was the differential regulation of two tests used for breast cancer patients. The two tests, MammaPrint and Oncotype Dx are regulated differently even though both aim to help doctors understand when patients should have follow-up chemotherapy after surgery. The company that markets MammaPrint, Agendia, chose to obtain FDA clearance for their test, but the company behind Oncotype Dx, Genomic Health, chose against it. Surprisingly, this decision did not substantially increase the number of patients who receive Oncotype Dx relative to MammaPrint.

Furthermore, the two tests do not always produce the same result, according to a research study. Several key question remain, such as:

Is the FDA-regulated test more accurate?
Does the more accurate test get more market share? Does FDA approval make a difference?
How should these tests, and ones like them, be regulated to reduce harm to patients?

The students hope that their case studies will serve as illuminating examples for stakeholders and help guide the conversation regarding federal regulation of LDTs.

When Bad Viruses Do Good

By Karl Bates

On March 31, 2015

In Biomedical Engineering, Cancer, Medicine, Neuroscience, Students

Guest post by Ted Stanek, Graduate Student in Neurobiology

Poliovirus binding to a receptor, the first stage in infection.

The polio vaccine was a medical triumph, single-handedly decreasing the number of polio cases in the world from more than 350,000 in 1988 to only 416 in 2013. Now, surgeons at Duke University are using the once universally feared virus to target another disease – cancer.

One of the big problems with cancer is that your body doesn’t know it’s dangerous. For most infections, your immune system learns to recognize what a dangerous or infected cell looks like. Cells infected by a virus will display protein markers which alert your immune system that they are infected. Invading bacteria also display similar markers, aiding the immune system in finding and targeting them.

But in cancer, your own cells appear just like they always do, even while they are multiplying uncontrollably. Your immune system has no way to distinguish these multiplying cells from healthy cells, and so it doesn’t know to attack the tumor.

In Fan Wang’s lab at Duke, we use the rabies virus and special dyes to trace the paths of individual neurons in a mouse’s brain.

A team at the Preston Robert Tisch Brain Tumor Center at Duke is looking to viruses to help the immune system find and kill tumor cells. If a virus could be made to only attack tumor cells, then infecting tumors with such a virus could help your immune system clear away tumors – whether benign or malignant.

It turns out the polio virus can do this. Because tumor cells are growing and multiplying rapidly, they look a lot like muscle cells in a healthy, growing child – polio’s prime target. Infection of these cells results in muscle loss seen in some children with the disease. From here polio can infect neurons that activate these muscles, causing paralysis. In that sense, it uses the same process of entry into the nervous system as the rabies virus, which I and others in the lab of Fan Wang here at Duke use to trace circuits in the brain.

Matthias Gromeier engineered a poliovirus to attack brain tumors.

Like the rabies virus, most of the machinery in the polio virus is made to target and reproduce in these growing cells, while only one gene causes the actual disease. To get around this, associate professor of neurosurgery Dr. Matthias Gromeier deleted this polio disease gene and replaced it with one for the common cold. When tested in monkeys, the virus was found to be effective in targeting and helping to clear out brain tumors without affecting the nearby healthy neurons.

Gromeier and Duke neurosurgeons are injecting a form of the polio vaccine directly into human brain tumors in a Phase I trial they hope will lead to approval as a cancer treatment – and so far they have had some encouraging successes.

The beauty of this treatment is that it might not be limited to brain tumors. Gromeier is planning to test the virus in future clinical trials against prostate cancer, lung cancer, colon cancer, and many others.

(CBS 60 Minutes just aired a special two-part segment on these experiments with polio virus. View them here.)

Got Data? 200+ Crunch Numbers for Duke DataFest

By Robin Smith

On March 23, 2015

In Computers/Technology, Data, Statistics, Students, Visualization

Photos by Rita Lo; Writing by Robin Smith

While many students’ eyes were on the NCAA Tournament this weekend, a different kind of tournament was taking place at the Edge. Students from Duke and five other area schools set up camp amidst a jumble of laptops and power cords and white boards for DataFest, a 48-hour stats competition with real-world data. Now in its fourth year at Duke, the event has grown from roughly two dozen students to more than 220 participants.

Teams of two to five students had 48 hours to make sense of a single data set. The data was kept secret until the start of the competition Friday night. Consisting of visitor info from a popular comparison shopping site, it was spread across five tables and several million rows.

“The size and complexity of the data set took me by surprise,” said junior David Clancy.

For many, it was their first experience with real-world data. “In most courses, the problems are guided and it is very clear what you need to accomplish and how,” said Duke junior Tori Hall. “DataFest is much more like the real world, where you’re given data and have to find your own way to produce something meaningful.”

“I didn’t expect the challenge to be so open-ended,” said Duke junior Greg Poore. “The stakeholder literally ended their ‘pitch’ to the participants with the company’s goals and let us loose from there.”

: Winners of best visualization: Greg Poore, Tori Hall, Michael Lin and David Clancy of the team Bayes’ Anatomy

: Winners of best insight:, Yang Su, Ruofei Wang, Yiyun Gu, Hong Xu and Yikun Zhou of the team Poke.R

: Winners of best use of outside data: Matt Tyler and Justin Yu of the team Type 3 Errors

As they began exploring the data, the Poke.R team discovered that 1 in 4 customers spend more than they planned. The team then set about finding ways of helping the company identify these “dream customers” ahead of time based on their demographics and web browsing behavior — findings that won them first place in the “best insight” category.

“On Saturday afternoon, after 24 hours of working, we found all the models we tried failed miserably,” said team member Hong Xu. “But we didn’t give up and brainstormed and discussed our problems with the VIP consultants. They gave us invaluable insights and suggestions.”

Consultants from businesses and area schools stayed on hand until midnight on both Friday and Saturday to answer questions. Finally, on Sunday afternoon the teams presented their ideas to the judges.

Seniors Matt Tyler and Justin Yu of the Type 3 Errors team combined the assigned data set with outside data on political preferences to find out if people from red or blue cities were more likely to buy eco-friendly products.

“I particularly enjoyed DataFest because it encouraged interdisciplinary collaboration, not only between members from fields such as statistics, math, and engineering, but it also economics, sociology, and, in our case, political science,” Yu said.

The Bayes’ Anatomy team won the best visualization category by illustrating trends in customer preferences with a flow diagram and a network graph aimed at improving the company’s targeting advertising.

“I was just very happily surprised to win!” said team member and Duke junior Michael Lin.

Joining the Team: Anika Ayyar

By Anika Ayyar

On February 22, 2015

In Biology, Computers/Technology, Engineering, Genetics/Genomics, Science Communication & Education, Students

By Anika Ayyar

Hi! My name is Anika Ayyar and I am currently a Duke freshman. I grew up in warm, lovely Saratoga, California, where I picked up my love for long distance running, organic farming, and the ocean. When I was 14, I moved to across the country to Exeter, New Hampshire to attend a boarding high school, and here I developed a deep interest in biology and medicine. Exeter’s frost and snow were far from the Cali weather I was used to, but my fascinating classes, caring teachers, and wonderful friends more than made up for the cold.

My sophomore semester abroad program at The Island School, on an island called Eleuthera in the Bahamas, certainly provided a welcome change to East coast weather as well. At the Island School I studied marine biology and environmental conservation, earned my SCUBA certification, and spent time with the local middle schoolers refurbishing a library and stocking it with books. I was also part of a research team that studied species richness and diversity on patch reefs off the coast of the island.

Dissecting fruit fly larvae under the microscope at the Seung Kim Lab at Stanford.

My marine research stint in the Bahamas drove me to join a molecular biology lab the summer after I returned; a decision that transformed my passion for science. At the Seung Kim Lab for Pancreas Development at Stanford University, I worked on a project that used binary systems to study the expression of specific genes related to insulin production and diabetes in fruit flies. I soon grew so immersed in my work that I wanted to share the project with others in the scientific community at Exeter, and my research mentors, biology professors, and I worked to create a novel course where other students could take part in the project as well. This unique research collaboration, called the “StanEx” project, proved to be a huge success, allowing other students to experience the trials and joys of real-world research while also generating Drosophila fly strains that were useful to the larger scientific community. If you are interested in reading more, check out my website about the StanEx project!

While my current interests lie more at the intersection of technology and medicine, I hope to be involved in equally compelling and fulfilling research here at Duke. Hearing about the various projects my professors are working on, and reading about the discoveries made in labs on campus, I have no doubt that this will be the case.

Outside of classes and research, I enjoy being part of the Duke Debate team, and Lady Blue, one of Duke’s all-female a cappella groups. You can often find me on the trails on a long run, or trying out a new dessert recipe I found on Pinterest. I am beyond excited to be a part of the research blogging team, and can’t wait to start attending talks and interviewing research personalities whose stories I can share with our readers!

Ben Wang: Food lover and undergraduate researcher

By sa160@duke.edu

On January 29, 2015

In Biology, Chemistry, Medicine, Students

Ben Wang in rural Appalachia Credit: Ben Wang

By Nonie Arora

Ben Wang, a senior Evolutionary Anthropology major from New Jersey, strongly believes we are what we eat. A foodie, scientist, and future health care practitioner, he thinks that changing food habits can improve our nation’s health.

“When we came to Duke, our summer reading book was Eating Animals,” he said. “I felt so many emotions while I was reading the book. It really impacted the way I think about food. In fact, I became a pescetarian (a fish-eating vegetarian).”

Freshman year, Wang knew he had this interest in food, but he didn’t know how to incorporate it into his academic world.

During his second year, Wang started to find his way. “I remembered the topic when I was hunting for a research lab, and started working in Dr. Tso-Pang Yao’s metabolism lab so that I could learn more about how nutrition directly impacts health,” he said.

Wang spent time investigating proteins that increase or decrease the amount of “mitochondrial fusion” that happens in cells. Wang explained that metabolism is how our bodies process food and distribute nutrients, and these compounds help in that process.

“I really enjoyed this lab because the topic was directly related to patient care and our research had direct pharmacologic applications,” Wang said.

Farm Fresh tomatoes! Credit: Ben Wang

In the summer of 2014, he pursued a Bass Connections fellowship in rural Appalachia, in one of the most impoverished counties in the US.

He participated in a Farm-to-Table partnership between local Appalachian farms and a middle school. This partnership was part of a broader program for Appalachian girls. He coordinated the logistics and ended up doing much of the culinary work for the partnership, cooking up delicacies with ingredients like swiss chard, beets, and kale.

“I really wanted to go all the way in introducing a fresh perspective to these women,” Wang said, “I had to convince the girls that these veggies would taste good.”

Farm to Table initiative in action. Credit: Ben Wang

They did not always like his creations.
He says one student told him, “I’m not going to eat this hippie food.”

But he persevered, and ultimately most of the girls were excited about what they had learned and reevaluated the way they ate.

Maintaining lasting gains will be difficult because much of the food would have been unaffordable to the girls on their own. In the town that they live in, the closest supermarket is a Walmart a half hour away. Other than that, there is a Dollar General and Hillbilly Market, neither of which stock fresh produce, according to Wang.

However, Wang thinks that showing these girls there are food options beyond those that they have experienced was valuable, and that they can choose to strive for them if they want to.

Changing eating habits, one delicious meal at a time. Credit: Ben Wang

As for Wang, he is headed to dental school in the fall and hopes to include nutritional awareness in his future practice to help his patients achieve better systemic health.

Behind the Scenes at Duke's Student-Run Science Journal

By sa160@duke.edu

On January 22, 2015

In Science Communication & Education, Students

By Nonie Arora

What do tuberculosis vaccines, water quality, and protein trafficking share in common? All may be featured in articles for the upcoming issue of Duke Science Review. I spoke with Matthew Draelos, co-editor-in-chief, and other publication team members.

Duke Science Review Publication. Credit: Nonie Arora

Draelos explained that the Duke Science Review deals with broad topics with an emphasis on review articles and draws from the undergraduate, graduate, and professional school communities.

Draelos’s motivations for leading the Duke Science Review stem from his previous research experiences. Draelos worked in an undergraduate lab for four years at NC State University. There, he felt integrated into the publication process in the laboratory of Dr. Gavin Williams. At Duke, he is excited to have the opportunity to get involved in a student-run science journal and take on a leadership role.

His interest in science is focused on pharmaceutical development, particularly antibiotics. He has worked previously with enzymes called polyketide synthases, which are nature’s machinery for making antibiotics. He hopes to someday develop novel chemical solutions to unsolved medical problems.

Students learn about the publication process. Credit: Nonie Arora.

“I think it’s important for students to publish their research primarily because in the current funding environment it’s publish or perish. This is increasingly true for young scientists. We must be able to write well, and the Duke Science Review establishes a risk-free forum for students to practice scientific writing,” Draelos commented.

A second reason he mentioned for enabling students to publish their work is that people spend considerable time and energy writing papers for courses, and a lot of that effort is wasted if only the professor is able to read their work. This journal is a way for people to spread their work to a larger audience and perhaps gain some additional recognition.

Lefko Charalambous, an editor for the journal, added that it is important to improve scientific communication and literacy in budding scientists. “It’s a way for us to appreciate what goes into producing a journal article and the reward from having it published at our age,” he said.

“We hope to enrich the scientific discourse, especially for freshmen and sophomores who are looking into scientific research and don’t know where to start,” Draelos said.

To submit an abstract for a potential report or article, check out their website.

iGEM: An Exciting Way to Merge Biology and Engineering

By Anika Radiya-Dixit

On January 13, 2015

In Biology, Biomedical Engineering, Computers/Technology, Engineering, Field Research, Genetics/Genomics, Students

Duke iGEM 2014 team with faculty advisors Nick Buchler, front left, and Charlie Gersbach, front right. Mike is behind Dr. Gersbach.

by Anika Radiya-Dixit

The International Genetically Engineered Machine (iGEM) competition is dedicated to education for students interested in the advancement of synthetic biology, in other words, taking engineering principles and applying them to natural sciences like biology.

Students in the competition explored using a gene or series of genes from E.coli bacteria to create biological devices for applications such as dissolving plastic or filtering water. In November 2014, the Duke iGEM team took part in the annual competition in Boston, proudly leaving with a gold medal on their work in 3D printing technology and DNA synthesis protocol.

This week, I contacted the iGEM team and had the opportunity to talk with one of the members, Mike Zhu, about his experience in the competition. Mike is currently a junior from Northern California studying Biomedical Engineering and Computer Science. He is enthusiastic about researching how biology and computer science interact, and is conducting research with Dr. John Reif on DNA technology. Mike is also involved with the Chinese Dance team, and enjoys cooking, eating, and sleeping. Below is an edited transcript of the interview.

How did you get interested in your project topic?

We wanted to build a binary response platform that uses logic gates or on-off switches in E. coli to make it easier to regulate genes. We used the CRISPr/Cas9 system that allows for specific targeting of any gene, and that enables synthetic biologists to create more complex gene circuits. Personally, I was interested in developing an infrastructure that allows engineering concepts to be applied to cells, such as creating code that allows cells to do arithmetic so they can keep track of the cells around them. I think applications like these open doors to a really cool field.

What was your best moment during the Boston competition?

The competition was four days long, but we had to come back early due to work and midterms, so we missed the last dance and dinner, but overall it was a lot of fun. There were multiple workshops and talks, and the one that stood out most to me was one by someone from MIT who designed a ‘biocompiler’ to take code specifying the behavior of cells [1]. It was essentially like creating a programming language for cells, and I thought that was really cool.

Tell me about someone interesting you met.

There were a lot of people from the industry who came by and asked about our project, and some of them wanted to recruit us for internships. At the competition, there were people from all over the world, and I liked best that they were friendly and genuinely interested in developing tools to work with cells.

Experiment work in a biology lab.

What was the hardest or most frustrating part of working on the project?

Lab work is always the most frustrating because you’re dealing with microscopic parts – things easily go wrong and it’s difficult to debug, so we ended up repeating the experiments over and over to work through it.

Are you continuing with the competition this year?

I’m working for Caribou Biosciences in Berkeley, one of the companies that wanted to recruit us during the competition. They are developing tech similar to what we did, so I enjoy that.

It’s a good thing to get into bioengineering. People are trying to make tech cheaper and easier so we can potentially do experiments in our garage – sort of like ‘biohacking’ or do-it-yourself-biology – and this still has a long way to go, but it’s really cool.

Mike Zhu, wearing the competition shirt.

Now that you’ve gone through the competition, what would you like to say to future students who are interested in applying their knowledge of BME learned at Duke?

There are a lot of clubs at Duke that are project-based, but these are primarily in Electrical Engineering or Mechanical Engineering, so the iGEM competition is – as far as I know – the only project-based club for students more interested in biology. You get funding, lab space, and mentors with a team of undergraduates who can work on a project themselves. It’s pretty rare for both PIs [Principal Investigators] to give the undergrads free reign to work on what they want, especially compared to volunteering in a lab. You also get a chance to present your project and meet up with other people, and you’re exposed to topics most students get to experience only in senior year classes. Overall, the club is a great way to be introduced to cutting edge research, and it’s a good opportunity for freshman to find out what’s going on in BME.

Learn More about the Duke iGEM team and project

[1] More about MIT’s Biocomplier can be read at http://web.mit.edu/jakebeal/www/Talks/IBE12-BioCompiler-Feedback-abstract.txt.

Multidimensional Student Maps Multidimensional Data

By Karl Bates

On January 1, 2015

In Computers/Technology, Engineering, Guest Post, Mathematics, Students

Grad Student Chris Trailie is a very three-dimensional person.

Grad Student Chris Tralie is a multi-dimensional person.

Guest post by Aravind Ezhilarasan, NC School of Science and Math

As I walked up to Gross Hall at Duke University, I felt nervous with butterflies in my stomach and honored to be able to interview Chris Tralie, a mathematician, computer scientist, musician, and music enthusiast. My hands were getting clammy, I was starting to have second thoughts about doing the interview, and I was shivering, not because of the chilly winter weather, but rather due to the contradicting feeling of giddy, childish excitement that was racing through me.

I had looked into his research, but had trouble making sense of it and was extremely puzzled as to how someone went from computer science to electrical engineering to mathematics.

With all this on my mind, I walked up the steps of Gross Hall.

Tralie, a doctoral candidate in Duke’s Electrical and Computer Engineering department, met me at the front door and led me up to a conference room where I asked him my first question: “Could you explain your research to me, a high school senior?” He hesitated a second, then jumped into the best lecture of my life.

Chris Tralie in the visible spectrum.

Tralie is currently working on the use of a simple geometric concept, loops, to identify and label songs by genre. He explained that he takes a song and tracks the loops in the song: intro, verse, chorus, then back to the verse (one loop), then back to the chorus, then back to the verse (two loops), etc.

He then takes the raw data he gets and turn it into a diagram. He explained that he maps the raw data out in a multidimensional environment, which has twelve dimensions to represent each note in a scale and more than forty other dimensions to represent different instrumentation in a song. It is impossible to visualize any object that has more dimensions than the three that we are acclimated to so Tralie then translates this multidimensional curve into three dimensions. You can check out the final product of this process for any song on his website, loopditty.net .

At this point of our exchange, my mind was well past blown.

Noticing my shocked, surprised, and ecstatic expression, he chuckled. I explained to him that I love what he is doing with this simple concept, but am still lost as to how one translates a multidimensional or high dimensional object into something three dimensional and perceivable. He then stepped back and explained this amazing process.

According to Tralie, when a light is far enough from an object, its rays are so close to being parallel that they are just taken to be parallel. When you shine this far-off light on a three-dimensional object, you get an analyzable two- dimensional object. In this same way, Tralie plays the role of the light for each extra dimension in his high dimensional models so he can simplify it down to a analyzable three dimensional object.

I asked him about his life and what made him switch from electrical engineering to computer science to a combination of computer science and mathematics. He then flashed back to his time as a kid. He explained that his goal in life as a young boy was to make video games. He always wanted to be the man behind the countless hours of entertainment he enjoyed. To reach this goal, he went into computer science and slowly realized electrical engineering was also a big player in reaching this goal. Through these experiences he went from computer science to electrical engineering. From there he went to a couple of transitional projects and eventually ended up at Duke University where he took on his long-lost hobby of mathematics and with the inspiration from his music appreciation days in his college eating club, he took on the genre labeling project.

Aravind Ezhilarasan

Finally, I asked him where he wanted his brainchild to be in the next three to five years. He explained that his genre labeling project is only the first step. He plans to take the looping concept that drives the project and apply it to many other scenarios. The point of his genre labeling project is to help him fully understand this concept and to work out all the possible problems that can occur. Eventually, he plans on using it in situations like security where instead of tracking loops in songs, it will track loops in security footage (someone walking on and then off the screen would be one loop).

As I left that building and made the trip back to the North Carolina School of Science and Mathematics, I felt content. I had walked into that building anxiously, feeling small and wondering what my interviewee would think of me when he realized I knew very little about his research and how someone switched between so many fields of science.

I walked out feeling well informed, understanding the transition in one’s thoughts and interests throughout the path of life, and with a new friend.

Passion, Modeling and Viruses are all Cool

By Karl Bates

On December 29, 2014

In Biology, Computers/Technology, Guest Post, Mathematics, Students

Guest Post By Jaye Sudweeks, NC School of Science and Math

Corona viruses like SARS (CDC image)

Viruses are very cool. Ashley Sobel taught me that.

Sobel is an MD/PHD student at Duke. She currently works in the Koelle Research Group, a group that focuses on using mathematical models to understand the “ecological and evolutionary dynamics of infectious diseases.”

When I asked Ashley what in particular drew her to infectious diseases, she had a ready answer. “Infectious diseases are pretty awesome. They have shaped more of human civilization than anything else. It’s very clear that the reason some wars came out the way they did isn’t because of good generals or good supply lines, but because of the viruses, pathogens and bacteria that people brought with them.”

Ashley Sobel is being groomed to be a physician-scientist.

Ashley’s interest in infectious diseases was piqued in high school, when the SARS virus hit. She recalls being intrigued that such a new phenomenon could have such a major impact.

It was this interest in SARS, along with participating in science Olympiad that drew Ashley to science. Ashley’s involvement in Science Olympiad began when the instructor found out that she was building her own cello out of a mannequin. “It’s name was Wilberta,” Ashley remembers fondly. “We gave it a coconut bra and a hula skirt.”

As a scientist, Ashley considers mathematics and modeling interesting tools to investigate infectious disease. “Modeling is basically taking key relationships that we know are true and putting them together in a mathematical context to see what we can learn about the underlying processes. You identify processes that you might not get by looking at the data.”

Ashley shared with me the process of building a model. The first thing to do when building a model, she explains, is to gain an understanding of the biology affecting the scenario. This should be followed by an examination of pre-existing models.

Next, it is important to make simplifications that allow your model to function, but don’t trivialize the subject matter. “There are a lot of standard assumptions,” she explains.

The time it takes to construct a model varies. Ashley has only recently completed a project that she started two years ago. “It can take a long time to identify the mathematics that will give you the patterns that you see in nature.”

Jaye Sudweeks

As a scientist, Ashley values the emphasis that the scientific community places on curiosity, a trait that she feels is looked down upon in other career fields. And, after just one conversation with Ashley, it is easy to see why she feels that way. Ashley is easily one of the most curious, passionate, and inspiring people I have ever had the privilege to meet. In the span of our brief meeting, Ashley sat crossed legged in her spinning office chair and taught me a couple of very important things.

Passion is cool. Modeling is cool. Viruses are cool.

Is it Computer Science or Biology? A Bit of Both

By Karl Bates

On December 26, 2014

In Animals, Biology, Guest Post, Mathematics, Students

Guest Post By Chichi Zhu, NC School of Science and Math

The National Evolutionary Synthesis Center (NESCent), is tucked away behind the supermarkets and youth-infested restaurants on Ninth Street in Durham. It’s a National Science Foundation brainchild with the purpose of consolidating data collected on small scales to help evolutionary biologists answer larger scale questions.

Allen Rodrigo directs NESCent and is a professor of biology at Duke

NESCent pursues a variety of missions, from answering these big ideas to connecting evolutionary science to linguistics and religious and cultural studies. Behind NESCent’s day-to-day function is evolutionary biologist Allen Rodrigo.

As a response to the question “so, what exactly is it that you do?” Rodrigo laughs. Here at NESCent, he oversees all of the programs, managing NSF grant money and keeping each part of the center on track with its mission. But NESCent is coming to the end of its funded run, and Dr. Rodrigo himself does far more than direct this innovative program.

Rodrigo is also a professor at Duke University and a computational evolutionary biologist. As a student, he was interested in three areas of study: mathematics, computer science, and biology. He continued pursuing all three tracks throughout his higher education, and allowed coincidence to launch him into his field today. The timing of his post-doc perfectly coincided with a late-1980s boom in technologic and scientific advances. With the invention of PCR and the subsequent increase in ability to study genetics, there came a demand for people with the skill and ability to conduct studies computationally, thus propelling Dr. Rodrigo into this growing field.

“There are many benefits to using computational methods,” Rodrigo said. “Suppose you want to compare two potential hypotheses on how a system might look, what patterns you might see. A computational biologist can help you with that.” He advocates for his area of study with a digestible list of its merits: “It helps experimentalists, it helps make inferences, and it helps make predictions about patterns.”

Today Rodrigo teaches classes at Duke, including courses on statistics for biologists and courses on computational science. He applies his passions for computational biology to his own research.

He is currently using computational study to track the evolution of traits of cancer related to their malignancy. “We start with a small set of cells and develop simulations that tell us how these cells change, grow, and divide,” Rodrigo said. “We can simulate how mutations accumulate, and can simulate, for a given collection of cells, what patterns of evolution you’d obtain.”

Chichi Zhu

Working with oncologists from Duke, his job is to use these computational and mathematical methods to search for patterns that oncologists can then use to collect laboratory data. “To do this all in a lab would take quite a long time,” he said. “To apply computational biology is much more efficient.”