Tag: Auslander

Wistar welcomes Dr. Noam Auslander as an assistant professor in the Cancer Center’s Molecular & Cellular Oncogenesis Program. She applies artificial intelligence (AI) through high-throughput computer approaches to interpret the very large sets of data biomedical research produces.

Q: What’s the role of artificial intelligence in biology?

A: Using AI, we can process big and complex datasets, integrate different data types, extract new knowledge, and identify patterns that describe specific features or outcomes that we are interested in. Using computing power, we try to identify complex patterns in the data to uncover biologically and clinically relevant information and help predict prognosis and treatment response. While AI has deeply transformed other fields, we are not exploiting its full potential in biology yet, but we’re getting there. For example, deep learning methods are currently outperforming any other approach to predicting protein structure.

Q: What attracted you to AI and machine learning?

A: I double majored in computer science and biology because I liked both disciplines. During my Ph.D. training in computer science, I specialized in computational biology and I realized that almost any biologic question could be tackled through AI and that computing power can help analyze very complex data sets.

Q: What are your research interests and goals?

A: I’m interested in how cancer evolves during disease progression. Over time, cancer cells accumulate mutations and other features that favor
their continued growth and survival and eventually promote metastasis. Cells carrying the most favorable alterations are selected, leading to the emergence of different populations. Deciphering this process has important implications for therapy response and resistance to treatment. I also study the evolution of viral infections. I approach these topics using artificial intelligence and develop new software and algorithms to answer different biologic questions.

Q: How will your research and expertise fit into Wistar’s research programs?

A: My research is very collaborative by nature: My lab won’t generate primary data from lab experiments. Instead, we will apply our computational expertise working with other teams to enhance the potential of their data. I see many promising opportunities for collaboration, for example with the Herlyn lab on immunotherapy in melanoma and the Zhang lab on ovarian cancer. I’m excited to join such a dynamic and collaborative environment.

Q: How will your work with scientists support what they do?

A: I think that AI can be useful for many ongoing research projects at Wistar. It can be used, for instance, to identify biomarkers, develop clinical predictors, and uncover deleterious alterations. We can utilize these tools to identify candidate genes or mutations that confer treatment sensitivity or resistance and to predict genomic features that enhance viral pathogenicity and infectivity. Therefore, with the expansive growth of genomic, molecular, and clinical data, machine and deep learning methods offer unique opportunities for biomedical research.

Q: Tell us a little about where you came from, your background, and your interests.

A: I grew up in Israel, where military service is mandatory for everyone, so it’s really nothing special. I served in the Intelligence Corps of the IDF between 2008-2010. My unit was in the School of Intelligence, and we worked on computer-based training projects, where I was team leader of computer graphics from 2009.

I absolutely love research. It’s so much fun that I consider my work also a hobby. I also enjoy sports: long distance running, skiing and snowboarding. Growing up in Israel you’re not exactly close to the mountains, but I used to go skiing in the Alps and loved it. I’ve found many great places in the U.S. too.

Many people unwind in front of the television after a long day. But Noam Auslander, Ph.D., who joined The Wistar Institute Cancer Center in June as an assistant professor, often spends the evening glued to the screen of her MacBook Pro laptop instead, looking for new insights into how tumors progress and cause disease.

“Sometimes I enjoy my work so much that it is my hobby,” Noam said. The most exciting moments are when, by using innovative algorithms that she builds, she starts to see patterns emerge from a data set that hint at an answer to one of her questions. The question she’s beginning to explore at Wistar is complicated — why some tumors metastasize while others do not, but Noam thinks enough data may be available, from the growing number of cancer patients getting genetic testing, to tackle it.

Joining the Community

Noam gravitated to Wistar because of its small environment, quite a contrast from the sprawling National Institutes of Health where she did her postdoctoral research. She felt Wistar would be the perfect place to foster opportunities to work with colleagues. “My work is dependent on collaborations,” Noam said. As a computational lab, she relies on data sets, and although many are publicly available, data that her colleagues have collected, both from patient samples and lab experiments, could greatly enhance her studies.

Collaborating with labs that conduct experiments, such as in cell lines and mice, is also critical for Noam to be able to test, and hopefully validate, what her algorithms show her in biological systems that mimic cancer processes. During her postdoc, for example, Noam and colleagues found that certain types of cancers harbor either high number of genetic mutations or aneuploidy, which is an abnormal number of chromosomes, but never both. It was a finding ripe to explore in cells, as a separate research group did, to identify possible new treatment strategies for aneuploidy cancer cells, which are particularly untreatable.

Bringing Together Computers and Biology

Growing up in Israel, Noam got a head start in computers. She was only 12 when she took her first elective course in the subject, like many of her peers. By the time Noam finished high school, she had a strong enough foundation in coding that she focused on computers during her mandatory two-year military service. But the work nearly zapped her passion. “It’s nice when you’re learning something in the beginning, but then you’re just doing the same thing over and over again,” Noam said.

Fortunately, Noam sought the advice of a friend who was getting his M.D.-Ph.D. Although Noam’s father was hoping she would follow that path and become a medical doctor, her friend listened to her interests — which included biology but not working with patients! — and instead suggested she combine computer science and biology. It was a revelation to Noam, and she headed into a dual degree at Tel Aviv University. The first three years were a slog, as computer science and biology were taught separately, unlike at many schools where they are melded into some type of bioinformatics program, and it was hard to see how the two could fit together. But Noam stuck it out and she was rewarded with the joy of finally learning how to apply algorithms to answer biological questions.

During the years at university, and then carrying out her Ph.D. at the University of Maryland and postdoc at NIH, Noam has witnessed a coming of age of the application of algorithms and artificial intelligence (AI) in biomedical research. “In some aspects of cancer research, it is on the verge, like in radiology,” Noam said. For example, AI can now be used clinically to analyze images to detect certain tumor types.

However, in the areas that Noam studies, genomics and omics data in general, she explained that AI has a lot of room for improvement, in accumulating sufficient data sets, in determining how to best represent the biological language of DNA, RNA and protein sequences in algorithms, and in making the processes of machine learning models understandable to clinicians who may one day rely on them to make treatment decisions. Noam hopes to help overcome some of these challenges, such as by creating algorithms that rely on more interpretable methods.

As she builds her lab at Wistar, Noam will set her sights on another pillar of Wistar’s research: infectious disease. She plans to use a method she developed during her postdoc to identify bacterial viruses, or bacteriophages, to look for new viruses in tumor cells. She suspects that there are many unidentified viruses out there and some may be present in cancer cells, which could either spur cancer progression or serve as a biomarkers of disease. “The original bacteriophage project was easier, but this is more interesting. It is a stepwise process to get there,” Noam said.

Already at Home

Noam will welcome the first postdoc and technician into her group this fall. They will work at stations in the lab with their own laptops — and the space will soon look like all the labs Noam has worked in over the years.

In her own office, Noam already feels settled in at her desk. The view from her windows is filled with lush trees. But as soon as those trees lose their leaves and it becomes winter, Noam looks forward to embarking on getaways for her second favorite activities after science: skiing and snowboarding. That is, if she can pull herself away from her laptop.

Written by Carina Storrs, Ph.D.