News

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.

Economic Markets and Biological Markets

In a similar manner to the ways in which countries make and trade goods, microbial cells within bacterial communities exchange metabolites to promote cell growth. This perspective could provide a way of studying microbial communities from the perspective of economics.

An article in the Wall Street Journal reports on a recent collaboration involving Columbia University Department of Systems Biology Assistant Professor Harris Wang and Claremont Graduate University economist Joshua Tasoff that identified some intriguing similarities between economic markets and the exchange of resources among microbes within bacterial communities. 

In an unusual marriage, biology and economics appear to be a match made in heaven.

Four years ago, two former roommates reunited at a friend’s wedding had time to catch up. The first, an economist, asked: “What are you working on?” The second, a biologist, answered: “How microbial communities interact. It’s kind of like in economics.”

And that’s when the intellectual sparks began to fly.

Chimpanzee

By using statistical methods to compare genomic data across species, such as chimpanzees and humans, the Przeworski Lab is gaining insights into the origins of genetic variation and adaptation. (Photo: Common chimpanzee at the Leipzig Zoo. Thomas Lersch, Wikimedia Commons.)

Launched approximately 100 years ago, population genetics is a subfield within evolutionary biology that seeks to explain how processes such as mutation, natural selection, and random genetic drift lead to genetic variation within and between species. Population genetics was originally born from the convergence of Mendelian genetics and biostatistics, but with the recent availability of genome sequencing data and high-performance computing technologies, it has bloomed into a mature computational science that is providing increasingly high-resolution models of the processes that drive evolution.

Molly Przeworski, a professor in the Columbia University Departments of Biological Sciences and Systems Biology, majored in mathematics at Princeton before beginning her PhD in evolutionary biology at the University of Chicago in the mid-1990s. While there, she realized that the availability of increasingly large data sets was changing population genetics, and has since been interested in using statistical approaches to investigate questions such as how genetic variation drives adaptation and why mutation rate and recombination rate differ among species. In the following interview, she describes how population genetics is itself evolving, as well as some of her laboratory’s contributions to the field.

Yaniv Erlich
Yaniv Erlich. Photo: Jared Leeds.

A new article published online in Nature Genetics reports that short tandem repeats, a class of genetic alterations in which short motifs of nucleotide base pairs occur multiple times in a row, play a role in modulating gene expression. Leading the study was Yaniv Erlich, an assistant professor in the Columbia University Department of Computer Science and core member of the New York Genome Center who recently joined the Center for Computational Biology and Bioinformatics.

As an article in Columbia Engineering explains, the findings reveal a new class of genome regulation.

Peter Sims, Sagi Shapira, and Harris Wang

Assistant Professors Peter Sims, Sagi Shapira, and Harris Wang recently moved into a new Department of Systems Biology laboratory space designed to facilitate the development of new technologies for biological and biomedical research. Photo: Lynn Saville.

The Columbia University Department of Systems Biology has opened a new experimental research hub focused on biotechnology development. Occupying one and a half floors in the Mary Woodard Lasker Biomedical Research Building at Columbia University Medical Center, the facility will promote the design and implementation of new experimental methods for the study and engineering of biological systems. It will also enable a substantial expansion of Columbia’s next-generation genome sequencing capabilities.

The first occupants of the new facility are the laboratories of Department of Systems Biology Assistant Professors Sagi Shapira, Peter Sims, and Harris Wang, along with the Genome Sequencing and Analysis Center of the JP Sulzberger Columbia Genome Center. The community is slated to grow, as currently unoccupied space will soon accommodate additional Columbia University faculty labs that are also developing new biotechnologies.