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Phyllis Thangaraj
Phyllis Thangaraj, MD/PhD student (Tatonetti lab)

Aspiring physician-scientists from Columbia's Vagelos College of Physicians and Surgeons presented their research posters at the 14th annual MD-PhD Student Research Symposium on April 25. Their research delved into a range of topics, including Alzheimer’s disease, stroke, and stem cells. The event included a guest lecture by an alumna about her own career path as a physician-scientist, and culminated in the poster session judged by MD-PhD alumni who currently work at the University. Department of Systems Biology’s Phyllis Thangaraj, an MD/PhD student in the Nicholas Tatonetti lab , was named one of five poster winners at the event. 

She presented work on applying machine learning methods to phenotype acute ischemic stroke patients in the electronic health records. In cohort research studies, it is essential to identify a large number of subjects in an accurate and efficient manner, but often this requires time-consuming manual review of patient charts. 

“We applied machine learning methods to data within a patient’s electronic health records to develop a high-throughput way to define research cohorts,” explains Thangaraj. “Our test case is in acute ischemic stroke. We extracted clues within a person’s medical record that required minimal data processing to classify those who have had a stroke. In a separate cohort, the UK Biobank, we were able to use our model to identify patients with self-reported stroke but no mention in their medical data with 65-fold better precision than random selection of patients.” Although stroke was the test case in this particular work, she explained that their workflow could be applied to identify patients for cohorts of other diseases, particularly when the dataset has missing data. 

Brian Ji Vitkup Lab
Brian Ji won Best Oral Presentation at Biennial Integrated Program Retreat; Visit the gallery for photos from the event.

Brian Ji , a combined MD/PhD student in Columbia’s Department of Systems Biology, delivered the winning oral presentation at the recent Biennial Integrated Program Retreat. Ji, who is a member of the Vitkup Lab, presented “Quantification of Human Gut Microbiota Variability Using Replicate Sampling,” and was one of six systems biology graduate students who delivered research presentations at the conference. 

Ji discussed a novel experimental and computational method he has developed to understand spatiotemporal dynamics of the human gut microbiome, as well as the technical noise tied to current human microbiome sequencing techniques. In addition to the human gut, the method, he says, is broadly applicable to other bacterial ecosystems and other sequencing-based studies. In the Vitkup Lab , Ji works on developing and utilizing quantitative approaches to reveal novel biological insights into bacterial ecology as well as cell physiology. His research interests also include exploring computational models and tools to study cancer metabolism at a global scale. In 2011, Ji received a prestigious Barry Goldwater Scholarship for his work on mathematical modeling to study impaired brain connectivity in epilepsy.  

Molly Przeworski Distinguished Columbia Faculty Award
Molly Przeworski

Molly Przeworski, PhD , professor of  biological sciences and of systems biology , has received the Distinguished Columbia Faculty Award for exceptional teaching. A leading population geneticist, Dr. Przeworski is one of eight recipients of the annual award, which recognizes faculty across a range of academic activities, including scholarship, University citizenship and professional involvement, with an emphasis on the instruction and mentoring of undergraduate and graduate students. 

The recipients this year were presented with the award at an April 11 event held at Columbia’s Italian Academy.

“It is wonderful to see the work we do teaching and mentoring graduate students recognized,” says Dr. Przeworski. “I have been really lucky to attract phenomenal students and postdocs, and find that interacting with them is one of the most rewarding aspects of what I do.”

According to one undergraduate referred to in the award citation, Dr. Przeworski “is definitely one of the best teachers I have ever been taught by.” The student also described her lectures as “well-designed” to build a keen understanding of and active engagement with the material. Columbia also lauded her for helping to launch the first annual New York area meeting in population genetics, successfully connecting researchers of varying career stages.

Dr. Przeworski's work aims to understand how natural selection has shaped patterns of genetic variation, and to identify the causes and consequences of variation in recombination and mutation rates, in humans and other organisms. She is the recipient of the Howard Hughes Medical Institute Early Career Scientist award, the Rosalind Franklin Young Investigator award, the Friedrich Wilhelm Bessel Research award and an Alfred P. Sloan fellowship. 

Poster winners with Department Chair Andrea Califano (far right), left to right: Sebastien Weyn-Vanhentenryck, Yun Hao and Jinzhou Yuan

Research diversity and innovation were the key themes at the Department of Systems Biology’s annual retreat. Held Sept. 18 in Tarrytown, N.Y., the retreat was attended by 145 guests and included a mix of faculty, students, post-docs, research scientists and department guests. A series of presentations showcased the collaborative projects underway in the Center for Cancer Systems Therapeutics (CaST), along with sessions by faculty about their ongoing research, for example, in the areas of computational genetics, complex predictive methods and cancer-related genomics. The all-day event also included a poster session and competition, highlighting the department’s pool of talented students and researchers.

Department chair Andrea Califano said his hope is that the annual retreat gives everyone a chance to “reflect on the various different studies and diverse approaches currently going on in the department.” 

Faculty judges named three winners of the poster competition, recognizing the work of students Yun Hao and Sebastien Weyn-Vanhentenryck and post-doctoral research scientist, Jinzhou Yuan.

Yun Hao, a PhD student in Nicholas Tatonetti's lab, looked into targeted therapy, an emerging treatment that uses chemicals to block cancer growth and metastasis by interfering with specific molecular targets. Current agents used in cancer treatment such as epidermal growth factor receptor inhibitors are limited by low efficacy and high toxicity to normal tissues. Hao focused on G-protein coupled receptors (GPCRs), the largest family of membrane receptors, which have not yet been used in target therapy. Hao built a computational workflow to identify GPCRs for cancer therapy, and in his research, showed that predicted GPCRs exhibit both high efficacy and low toxicity levels, offering a new direction for the development of cancer drugs.

Classroom

The Department of Systems Biology is pleased to announce a new partnership with Columbia University’s School of Professional Studies to offer postbaccalaureate education in systems biology. The first course, titled Systems Biology: Blueprint for a 21st Century Scientific Revolution, is now accepting registrations for the spring 2017 semester.

The new course will provide a Master’s level overview of how systems biology is helping to address today’s grand challenges in biomedical research, what it can realistically be expected to achieve, and where it promises to have the most significant impact. Combining critical readings, discussions, tutorials, presentations, projects, and other activities, the course is designed for anyone interested in understanding the implications of systems biology across the sciences — including how it is affecting such fields as precision medicine, vaccine and antibiotic development, agriculture, science policy, and regulation.

Best Poster Winners
At this year's retreat Alexander Hsieh, Rotem Rubinstein, Jinzhou Yuan, and Jiguang Wang (clockwise from top left) were named winners in the Best Poster Competition.

On September 15, 2016, members of the Columbia University Department of Systems Biology gathered in Tarrytown, New York for the Department’s annual retreat. Although the tranquil setting overlooking the Hudson River was familiar, the event’s timing was new, taking place for the first time at the beginning of the academic year to enable first-year graduate students to become acquainted with the Department as they begin their studies. With a full day of scientific talks, a poster session, and ample time for informal conversation, the retreat provided an up-to-date survey of the diverse research taking place in the Department's laboratories.

In introductory remarks, Department Chair Andrea Califano celebrated the retreat as an important annual meeting that provides “a chance to bring our heads together and think about what we are as a community.” He then gave a brief update on recent developments in the Department — including the interdisciplinary and collaborative nature of its research, its growing emphasis on technology development, the high publishing productivity among its investigators, and its successful pipeline of funded grants.

Among these is a new U54 grant that has enabled the creation of the Center for Cancer Systems Therapeutics (CaST). Shannon Hughes, a program officer in the National Cancer Institute’s Division of Cancer Biology, followed Dr. Califano at the podium to introduce the new Cancer Systems Biology Consortium, of which CaST is one of four founding centers.

Following her remarks, Peter Sims, who recently became director of the Department of Systems Biology’s Graduate Program, discussed recent changes in the systems biology PhD track’s curriculum and requirements and the launch of a new faculty research seminar.

Staphylococcus epidermis
Interactions between human cells and the bacteria that inhabit our bodies can affect health. Here, Staphylococcus epidermis binds to nasal epithelial cells. (Image courtesy of Sheetal Trivedi and Sean Sullivan.)

Launched in 2014 by investigators in the Mailman School of Public Health, the CUMC Microbiome Working Group brings together basic, clinical, and population scientists interested in understanding how the human microbiome—the ecosystems of bacteria that inhabit and interact with our tissues and organs—affects our health. Computational biologists in the Department of Systems Biology have become increasingly involved in this interdepartmental community, contributing expertise in analytical approaches that make it possible to make sense of the large data sets that microbiome studies generate.

Cluster computer

Students participating in a new course gain experience using the Department of Systems Biology's computing cluster, a Top500 supercomputer dedicated to biological research.

As more and more biological research moves to a “big data” model, the ability to use high-performance computing platforms for analysis is rapidly becoming an essential skill set. To prepare students to work with these new tools more successfully, the Columbia University Department of Systems Biology recently partnered with the Mailman School of Public Health in launching a new graduate level class focused on providing a strong grounding in the fundamental concepts behind the technology.

Columbia University iGEM Team 2015

The Columbia University 2015 iGEM Team (l-r): Hudson Lee, Suppawat Kongthong, Jacky Cheung, Kenya Velez, Samuel Magaziner, and faculty moderator Harris Wang.

A team of undergraduate students based at Columbia University for the first time participated in this year’s International Genetically Engineered Machine Foundation (iGEM) competition. Supervised by Department of Systems Biology Assistant Professor Harris Wang, the team spent this past summer developing a project that used synthetic biology methods to engineer an edible, probiotic consortium of bacteria that could regulate hunger and digestion. In September they presented their results at the iGEM Giant Jamboree in Boston, MA, where they received a silver medal for their efforts. (For more informtion about their project, see the Columbia iGEM Team website.)

“I think it’s fantastic that this ambitious group of undergraduates worked so hard to represent Columbia University on this international stage,” says Dr. Wang. “Columbia has one of the great undergraduate colleges, and now that we have a critical mass of interested students and faculty laboratories with expertise in synthetic biology, we think iGEM offers a valuable opportunity to compete with and learn from teams at other leading institutions.”

Deep sequencing class

A new team-taught course covers both the experimental and analytical basics of next-generation sequencing. Assistant Professor Chaolin Zhang led the discussion in a recent class. Photo: Lynn Saville.

As the cost of next-generation sequencing has fallen, it has become a ubiquitous and indispensable tool for research across the biomedical sciences. DNA and RNA sequencing — along with other technologies for profiling phenomena such as de novo mutations, protein-nucleic acid interactions, chromatin accessibility, ribosome activity, and microRNA abundance — now make it possible to observe multiple layers of cellular function on a genome-wide scale.

Regardless of a biologist’s chosen area of investigation, such methods have made it possible to explore many exciting new kinds of problems. At the same time, however, it has also dramatically transformed the expertise that young scientists need to develop in order to participate in cutting-edge biological research. Bringing students up to speed with the pace of change in next-generation sequencing has posed a particular challenge for educators.

Now, a new multidisciplinary, graduate-level course organized by the Columbia University Department of Systems Biology is enabling young investigators to begin incorporating these powerful new tools into their studies and future research. Designed by assistant professors Yufeng Shen, Peter Sims, and Chaolin Zhang, the course covers both the experimental principles of next-generation sequencing and key statistical methods for analyzing the enormous datasets that such technologies produce. In this way, it gives students a strong grounding in principles that are critical for more advanced graduate courses as well as the ability to begin applying deep sequencing technologies to investigate the questions they are interested in pursuing.

As Dr. Sims explains, “Whether you are a graduate student in systems biology, biochemistry, or microbiology, the chance that you are going to be doing next-generation sequencing is pretty high. At the same time, it’s completely not taught at the undergraduate level. There is no text book nor is there any time in a typical undergraduate biology curriculum to get into this in any kind of detail. Even at top-tier universities students come into graduate school without having any experience with it, and often they’re expected to jump right into this kind of research. We decided that this was a problem we had to fix.”

Electronic media offer valuable tools for learning, but what is the best way to integrate these technologies within the traditional university setting?  Brent Stockwell, a faculty member in the Columbia University Department of Systems Biology, recently asked himself this question about blended learning, an educational approach he had begun incorporating into his undergraduate biochemistry class. As Columbia News reports, the results of this investigation have been published in the journal Cell:

Alex Lachmann
Alex Lachmann during his presentation to the RNA-Seq "boot camp."

In June 2015, the Columbia University Department of Systems Biology held a five-part lecture series focusing on advanced applications of RNA-Seq in biological research. The talks covered topics such as the use of RNA-Seq for studying heterogeneity among single cells, RNA-Seq experimental design, statistical approaches for analyzing RNA-Seq data, and the utilization of RNA-Seq for the prediction of molecular interaction networks. The speakers and organizers have compiled a list of lecture notes and study materials for those wishing to learn more. Click on the links below for more information.