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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.

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.