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Newly Tenured Faculty
Awarded tenure this year in the Department of Systems Biology, left to right: Dr. Nicholas Tatonetti, Dr. Yufeng Shen, and Dr. Chaolin Zhang.

Congratulations to Drs. Yufeng Shen, Nicholas Tatonetti, and Chaolin Zhang of the Department of Systems Biology, who have been awarded tenure and promoted to associate professor. Their new appointments are effective July 1, 2019. 

Yufeng Shen, PhD

Dr. Shen joined Columbia University Irving Medical Center in 2011 as an Assistant Professor in Systems Biology and Biomedical Informatics. He directs a research group focused on studies of human biology and diseases using genomic and computational approaches. They are developing new methods to interpret genomic variations by machine learning based on biological mechanisms, and using these methods in large-scale genome sequencing studies to identify new genetic causes of human diseases, such as autism, birth defects, and cancer. His group also works on modeling of clonal and transcriptional dynamics of immune cells to improve our understanding of human adaptive immune system under normal and clinical conditions. Dr. Shen serves as an Associate Director of the JP Sulzberger Columbia Genome Center, a member of the Program in Mathematical Genomics, and an adjunct member of Columbia Center for Translational Immunology. 

Nicholas Tatonetti, PhD

Dr. Tatonetti, whose primary appointment is in the Department of Bioinformatics, has an interdisciplinary appointment with both the Departments of Systems Biology and Medicine. Dr. Tatonetti’s lab specializes in advancing the application of data science in biology and health science. His group integrates their medical observations with systems and chemical biology models to not only explain drug effects, but also to gain further understanding of basic biology and human disease.

Columbia researchers have learned why some glioblastomas—the most common type of brain cancer—respond to immunotherapy. The findings, reported by the CUIMC Newsroom, could help identify patients who are most likely to benefit from treatment with immunotherapy drugs and lead to the development of more broadly effective treatments.

The study, led by Raul Rabadan, PhD, professor of systems biology and biomedical informatics at Columbia University Vagelos College of Physicians and Surgeons and the Herbert Irving Comprehensive Cancer Center, was published online in the journal Nature Medicine

Fewer than 1 in 10 patients with glioblastoma­ respond to immunotherapy, which has shown remarkable success in the past few years in treating a variety of aggressive cancers. But there has been no way to know in advance which glioblastoma patients will respond. Like many other cancers, glioblastomas are able to prevent the immune system from attacking cancer cells. Cancers sometimes put the brakes on the immune system by acting on a protein called PD-1. Immunotherapy drugs called PD-1 inhibitors are designed to release those brakes, unleashing the immune system. Given the success of PD-1 inhibitors in other cancers, doctors were hopeful that the immunotherapy drugs would help patients with glioblastoma. 

To understand why only a few of these tumors respond to the immunotherapy drugs, Dr. Rabadan’s team took a comprehensive look at the tumor microenvironment—which includes the tumor itself and all of the cells that support it—in 66 glioblastoma patients before and after treatment with PD-1 inhibitors (nivolumab or pembrolizumab). Of these, 17 had a response to the drugs of six months or longer.

Nonresponsive tumors had more mutations in a gene called PTEN, which led to higher levels of macrophages, immune cells that usually help the body fight bacteria and other invaders. But in glioblastoma, the macrophages release a number of growth factors that promote the survival and spread of cancer cells.

Tatonetti Heritability Image

Each subgraph in this image is a family reconstructed from EHR data: Each node represents an individual and the colors represent different health conditions. (Figure: Nicholas Tatonetti, PhD, Columbia University Vagelos College of Physicians and Surgeons).

Acne is highly heritable, passed down through families via genes, but anxiety appears more strongly linked to environmental causes, according to a new study that analyzed data from millions of electronic health records to estimate the heritability of hundreds of different traits and conditions. 

As reported by the Columbia Newsroom, the findings, published in Cell by researchers at Columbia University Irving Medical Center and NewYork-Presbyterian could streamline efforts to understand and mitigate disease risk—especially for diseases with no known disease-associated genes.

“Knowledge of a condition’s heritability—how much the condition’s variability can be attributed to genes—is essential for understanding the biological causes of the disease and for precision medicine,” says study co-leader Nicholas Tatonetti, PhD , the Herbert Irving Assistant Professor of Biomedical Informatics at Columbia University Vagelos College of Physicians and Surgeons and an assistant professor of systems biology. “It is clinically useful for estimating disease risk, customizing treatment, and tailoring patient care.”

May 7, 2018

From Code to Cure

Columbia Magazine

Published Spring 2018 cover story , Columbia Magazine

As reported by David J. Craig, senior editor at Columbia Magazine , we are living in the age of big data, and with every link we click, every message we send, and every movement we make, we generate torrents of information. In the past two years, the world has produced more than 90 percent of all the digital data that has ever been created. New technologies churn out an estimated 2.5 quintillion bytes per day. 

Today, researchers at Columbia University Irving Medical Center (CUIMC) are using the power of data to identify previously unrecognized drug side effects; they are predicting outbreaks of infectious diseases by monitoring Google search queries and social-media activity; and they are developing novel cancer treatments by using predictive analytics to model the internal dynamics of diseased cells. These ambitious projects, many of which involve large interdisciplinary teams of computer scientists, engineers, statisticians, and physicians, represent the future of academic research.

Craig covers Dr. Nicholas Tatonetti's work involving prescription drug safety and his innovative use of digital health and clinical records and Dr. Andrea Califano's unconventional computational approaches in advancing cancer research.

To read the full article , visit the online issue of Columbia Magazine

Faculty

Dennis Vitkup

Associate Professor, Department of Systems Biology
Associate Professor, Department of Systems Biology

Faculty

Nicholas Tatonetti

Herbert Irving Assistant Professor of Biomedical Informatics
Director of Clinical Informatics, Herbert Irving Comprehensive Cancer Center

Herbert Irving Assistant Professor of Biomedical Informatics
Director of Clinical Informatics, Herbert Irving Comprehensive Cancer Center

Faculty

Yufeng Shen

Associate Professor, Department of Systems Biology
Associate Director

Faculty

Raul Rabadan

Professor, Department of Systems Biology

Co-director, Next-Generation Sequencing

Faculty

Aris Floratos

Executive Research Director, Center for Computational Biology and Bioinformatics
Executive Research Director, Center for Computational Biology and Bioinformatics

Faculty

Andrea Califano

Chair, Department of Systems Biology
Director, JP Sulzberger Columbia Genome Center