IICD Newsletter March 2021

April 10, 2021
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March 1st, 2021
 
Andrew J. Blumberg, PhD: Diving into Cancer Genomics With Topology 
Written by Meeri Kim, PhD
A chance occurrence at a workshop inspired an interest in cancer genomics for mathematician Andrew J. Blumberg, PhD, the new Herbert and Florence Irving Professor of Cancer Data Research at the Herbert and Florence Irving Institute for Cancer Dynamics (IICD). He had organized a session on his area of expertise — topological data analysis, a field that uses advanced mathematical tools to extract information from complex datasets — when burst pipes damaged some of his colleagues’ offices. 
“I ended up sharing an office with Raúl Rabadán, a cancer genomics person and computational biologist at Columbia,” says Dr. Blumberg, who joined the University in January as a Professor of Mathematics and Computer Science. “We started talking, ended up doing a bunch of projects, and eventually wrote a book together. That got me very interested in applications coming from cancer genomics and evolutionary biology more broadly.”

Originally trained as an algebraic topologist, Dr. Blumberg began his career leveraging advanced algebra to study shapes and spaces. His long-standing interest in computers led him to topological data analysis as a postdoctoral fellow at Stanford University. This relatively new field uses algorithms from algebraic topology to tease out mathematical associations or patterns in the shape of data from complex systems. 

“When it comes to data analysis, you want a signal that’s reliable and actually means something as opposed to being a result of noise or sampling variability,” he says. “Because, of course, it’s very easy to fool yourself and see things in the data that aren’t there. There is a lot of pressure that pushes people in that direction, and so I’m very interested in methodological questions about how to avoid that kind of problem.”

He comes to Columbia from the University of Texas, Austin, where he served as a Professor of Mathematics and worked on the foundations of topological data analysis. As an endowed professor, he will spearhead the mission of the IICD and automatically becomes a member of the Herbert Irving Comprehensive Cancer Center (HICCC). He also is affiliated with the Center for Topology of Cancer Evolution and Heterogeneity at Columbia, which is co-directed by Rabadán. 

In the past, Dr. Blumberg has applied topological data analysis and other mathematical methods to cancer genomics to uncover hidden clues that may provide keys to the development, growth, and treatment of the disease. For example, he worked on a project that found that genomic architecture can inform targeted therapeutic interventions for patients with glioblastoma, a common and aggressive type of brain tumor. He also contributed to work dedicated to better understanding how glioblastoma evolves over time and throughout treatment, which identified genetic alterations associated with relapse.

His research interests have expanded into the realm of evolutionary biology as well. In 2019, Dr. Blumberg lent his expertise on geometric data analysis for a high-profile study published in Science on butterflies. This work introduced a new method of detecting the movement of genetic material between species, resolving some long-standing questions about butterfly evolution in the process. 

As the first member of the IICD recruited as a tenured professor, he is excited to continue such interdisciplinary research while at Columbia. He also hopes to help shape the future direction of the Institute and raise its profile both within the University and to the outside world by holding working groups and seminars. 

“The IICD, which itself sits across lots of fields, is a great place to be for this kind of cooperative research,” says Dr. Blumberg. “I’ve noticed a very explicit effort here to reach across to different parts of the University and have these kinds of collaborations with people from various parts of the medical school, hospitals around the city, and other departments.”
Announcements
 
Congratulation to our affiliate members Ben Raphael and Scott Fraser
Ben Raphael, PhD, Professor of Computer Science, Princeton University, the 2021 recipient of the ISCB Innovator Award.
 
 
Scott Fraser, PhD, Provost Professor of Biology and Bioengineering; Elizabeth Garrett Professor of Convergent Bioscience, Director of Science Initiatives, University of Southern California, awarded Edwin G. Conklin Medal by the Society for Developmental Biology
Welcome José L. McFaline-Figueroa
 
José L. McFaline-Figueroa, PhD joined the department of Biomedical Engineering in January 2021 as an Assistant Professor. We welcome José as an associate member in the Herbert and Florence Irving Institute for Cancer Dynamics. His work aims to define the molecular changes that cancer cells undergo in response to therapy and the genetic requirements of that response. His laboratory develops and applies single-cell genetic and chemical genomic tools to generate these maps of cellular response. The goal of his laboratory is to leverage this information to arrive at new treatment strategies for tumor types that frequently fail standard-of-care.
Welcome Xueer Chen
 
We would like to welcome Xueer Chen as a Postdoctoral Research Scientist in the Azizi lab. Xueer graduated from University of Pittsburgh under the mentorship of Xinghua Lu. She trained as a Computational Biologist and will apply her expertise of computational analysis of single-cell data as well as machine learning techniques such as topic modeling and causal inference to cancer immunology.
Job opportunities
 
Group Leader Positions in Computational Biology - Human Technopole in Milan

Particular interest around the topics of computational genomics, machine learning for multi-omics, single-cell approaches and digital pathology. See more about this opportunity here.

Postdoctoral positions available - Modeling Immunological Memory

Immunological memory is a complex system that is highly dynamic in time and space, involving multiple cell populations that compete, self-renew, turn over, and shift in phenotype and repertoire diversity over a person’s lifetime. The Yates group has openings for postdoctoral positions, using mathematical and computational methods to characterize the dynamic structure of T and B cell memory in various settings. Expertise in immunology is an advantage but not required. See more about this opportunity here, or to make an informal inquiry, email [email protected] 

Program Manager, Outreach and Communication

Under the supervision of the Chief of Staff, the Program Manager, Outreach and Communication will spearhead the communication and outreach endeavor of IICD. S/he will develop and cultivate collaborative relationships with inside and outside the Columbia community, showcase and highlight the Institute's strengths and oversee the education program of the Institute. For more information click here.

Staff Associate III

The Computational Cancer Biology Laboratory and the Laboratory for Synthetic Organogenesis at Columbia University are jointly seeking a Staff Associate III to assist with ongoing research in cancer biology in both labs as well as with collaborative projects between the two labs. For more information and application here.
 
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