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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.

Peter Sims & Jinzhou Yuan

Assistant Professor Peter Sims and postdoctoral research scientist Jinzhou Yuan displaying their platform for automated single cell RNA-Seq. Photo: Lynn Saville.

RNA sequencing (RNA-Seq) has become a workhorse technology for research in systems biology. Unlike genome sequencing, which reveals a sample’s DNA blueprint, RNA-Seq catalogs the constantly changing transcriptome; that is, it itemizes and quantifies the complete set of messenger RNA transcripts that are present in cells at a specific time and under specific conditions. In this way, RNA-Seq makes it possible to investigate how the information encoded in the genome is functionally transformed into observable traits, and provides valuable data for defining and comparing different biological states.

Conventional RNA-Seq generates an average summary of mRNA abundance across all of the cells in a sample. Recent research, however, has created a demand for higher resolution technologies capable of generating mRNA profiles at the level of single cells. In cancer biology, for example, there is an increasingly acute awareness that gene expression in the cells that make up malignant tumors is highly heterogeneous. This suggests that in order to understand how the cells work together to drive a tumor’s cancerous behavior, scientists need better methods for characterizing the entire ecology of cells of which it is made. Being able to quantify differences in gene expression cell by cell could be one valuable way to explore such complex environments and understand how they sustain malignancy.

Although several single cell RNA-seq technologies have been unveiled in the past two years, they are expensive to operate and are not optimized to produce data on the scale that is required for systems biology research, particularly in tissue specimens with limited numbers of cells. In a new paper just published in the journal Scientific Reports, however, researchers in the laboratory of Department of Systems Biology Assistant Professor Peter Sims describe a novel approach that offers several important advantages over other existing methods.

The new, automated platform builds on previous innovations in the Sims Lab to offer a cheap, efficient, and reliable way to simultaneously measure gene expression in thousands of individual cells from a single tissue sample. Using custom designed microwell plates, microfluidics, temperature control systems, and software, the technology captures, tags, and generates a readout of the complete transcriptome in each cell, providing robust data that can then be analyzed to distinguish functional diversity among the cells in the sample. Already, the technology is playing a key role in several research projects being conducted in the Department of Systems Biology and promises to become even more powerful as the field of single cell genomics continues to evolve.

Calendar

The Department of Systems Biology is pleased to announce the speakers in its 2016-2017 Seminar Series. The seminar series features leading investigators working in a diverse set of fields, including epigenomics, gene expression regulation, regulatory elements, evolutionary biology, cancer systems biology, and developmental biology, among others. Please save the dates!

All events will be held in the Department of Systems Biology Common Room (ICRC 816), unless indicated otherwise. Additional details about these events will be provided at the links below as they become available.

For a continually updated calendar of all Department of Systems Biology events, and to see an archive of past seminars, visit systemsbiology.columbia.edu/events.

Swarmbots

In a recent paper published in Molecular Systems Biology, Kam Leong describes a two-compartment microfluidic device that consists of a chamber within which is embedded a "microbial swarmbot" that is isolated by a permeable hydrogel shell. In collaboration with Lingchong You (Duke University), Leong used the device to regulate the dynamics of a population of bacteria containing a genetically engineered switch that reacts to population size. The scale bar in panel 1 represents a length of 250 micrometers.

With a restless curiosity, Kam Leong always seems to be on the lookout for new problems to solve. A versatile biomedical engineer originally trained in chemical engineering, he has developed an impressive array of innovative nanotechnologies that have opened up new opportunities in biomedical research and drug delivery. 

The most widely known of his designs resulted from his work as a postdoc in the laboratory of MIT’s Robert Langer. While there, Leong played a critical role in the development of Gliadel, a controlled-release therapy that uses biodegradable polymer particles to deliver an anticancer drug to a brain tumor site following surgery. Since then his name has appeared on more than 70 patents covering a wide range of inventions — from microfluidics technologies, to scaffolds for growing organic tissues, to nanoscale fluorescent probes, to a method that uses nanoparticles instead of viruses for the oral delivery of gene therapies. These achievements have gained him widespread respect within the engineering community, as evidenced by his 2013 election to both the National Academy of Engineering and the National Academy of Inventors.

Dr. Leong joined Columbia University in 2014. Although his primary affiliation is with the Department of Biomedical Engineering, he was also attracted by the chance to assume an interdisciplinary faculty appointment in the Department of Systems Biology. Since his arrival he has been developing collaborations with several Systems Biology faculty members as well as other scientists at Columbia University Medical Center, and plans are underway for his lab to move into the Lasker Biomedical Research Building to better facilitate interactions with systems biology and clinical investigators. In the following interview, Leong describes why opportunities to interact with scientists in other disciplines is so important to his work, and how the kinds of technologies he has developed could be relevant for systems biology research, as well as for improving treatment of human diseases.

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.