Skip to main content

Tag: Auslander

Scientists Drive Innovation at Wistar’s Ellen and Ronald Caplan Cancer Center

Written by The Wistar Institute on . Posted in Featured News.

Wistar continues to be a dynamic environment prepared to tackle biomedical challenges in a collaborative, innovative, and inclusive culture. Read more about our Ellen and Ronald Caplan Cancer Center commitment to scientific career development, a diverse research community, and how previously introduced recruits are settling in and advancing impactful science.

ENHANCING CAREERS AND EXPANDING DIVERSITY

Italo Tempera, Ph.D., newly appointed Associate Director for Cancer Research Career Enhancement, was a postdoctoral fellow at Wistar and returned as an associate professor in the Gene Expression and Regulation Program in 2020. His research focuses on epigenetic mechanisms behind Epstein-Barr Virus (EBV). He was recently named associate director for Cancer Research Career Enhancement.

Tempera considers the time he spent at Wistar to be formative. With its very collaborative introductory environment, Wistar is an “… opportunity for our students not only to learn about our science but to get in contact with scientists.”

Furthermore, he outlines what he would like to accomplish in his new role. “We’re outstanding scientists and we have excellent mentors. The opportunities for our trainees to do an internship with different departments is something we want to push forward, and we want to expand the Cancer Biology Ph.D. program that we have now with Saint Joseph’s University.”

He shares that Wistar gave him the opportunity to grow as a scientist and advance in his research career. “When someone asks what was one of the most important aspects of a scientist’s pre- or post-doctoral training, my goal is for the trainee to think back and reply that being at Wistar has made all the difference.”

Jessie Villanueva, Ph.D., newly appointed Associate Director for Diversity, Equity, and Inclusion, joined Wistar first as a postdoctoral fellow and then was appointed assistant professor in the Molecular and Cellular Oncogenesis Program. Her work aims to identify targets for therapy to treat melanoma.

“Diversity leads to innovation and scientific excellence. New discoveries and scientific breakthroughs often rely on collaborations, and diverse teams are more creative and resourceful,” she shares.

For her new role, Villanueva aims to lead and inspire everyone at Wistar to integrate inclusion, diversity, and equity into all facets of the Institute. “Our goal is to continue fostering an inclusive community where everyone can develop to their full potential while contributing to Wistar’s mission of scientific discoveries.” To accomplish this, she plans to work with leaders and stakeholders across the Institute to identify challenges and areas for
improvement and propose strategies to address them.

“Diversity supports Wistar’s mission,” Villanueva asserts. She elaborates that many of the Institute’s scientific breakthroughs are largely impactful for biomedical sciences and human health, and these discoveries rely on “… outstanding scientists, trainees and staff with diverse backgrounds and skills who support Wistar’s goals wholeheartedly.”

ADVANCING IMPACTFUL SCIENCE

Nan Zhang, Ph.D., Assistant Professor, Immunology, Microenvironment & Metastasis Program, joined Wistar in September 2021 as an assistant professor and currently researches how immune cells play a role in tumor growth in abdominal cancers.

“Studying disease was always one of my passions,” Zhang shares as he describes both a personal and professional draw to cancer research. He began his career studying the immune system — particularly macrophages, a special population of white blood cells that removes unwanted materials in the body like harmful microorganisms or dead cells.

Upon completion of his postdoctoral position, Zhang felt that cancer in the peritoneal space — the area of the body encompassing the abdomen and the organs within it — would be a great direction to pursue for his future career because of its unique complexity and how it’s less understood relative to other focus areas for cancer research. This is what he works on now at Wistar.

Immersed in the Institute’s world class techniques, resources, and renowned scientists, Zhang continues to push forward his research to tackle how to use specialized cells called macrophages to combat tumors as a checkpoint therapy for cancer. He is also investigating immunological questions about the microenvironment of the peritoneal space and how this knowledge can help inform therapeutics and treatment development.

He shares, “Wistar is competitive, and the support in the Institute for junior faculty is great. We have meetings every week and this is an environment I really wanted for my career and research.”

Noam Auslander, Ph.D., Assistant Professor, Molecular & Cellular Oncogenesis Program, joined Wistar in June 2021 as an assistant professor and conducts her research at the intersection of computer science and biological science. She uses machine learning to investigate genetic factors underpinning cancer evolution to improve diagnostics and therapeutics.

“I work on cancer and viruses. Both are complex and have high mutation rates. As a computational scientist, it’s very interesting because there are a lot of computational challenges that can be investigated,” Auslander comments.

She joined The Wistar Institute because of its reputation and expertise, particularly in researching both cancer and viruses. She shares her experience during her first year, “It’s a small institute with a lot of opportunities to collaborate. It’s a very good environment and people are very helpful and supportive.”

Simultaneous to establishing and expanding her lab group, Auslander is currently looking into improving clinical prognosis to cancer and other diseases by uncovering unknown infectious agents and therapeutic biomarkers. To accomplish this, her lab applies the power of advanced computational platforms to very intricate and complex biomedical data to make these predictors of treatment responses more biologically interpretable. She says, “My main focus at the moment is to train my growing lab and develop frameworks to identify new viruses and eventually new microbiomes in cancer.”

Dr. Noam Auslander

Dr. Noam Auslander: New Faculty Addition Brings Artificial Intelligence Research to Wistar

Written by The Wistar Institute on . Posted in Featured News.

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.

Dr. Noam Auslander

Motivated By the Hard Questions in Cancer Research, Noam Auslander, Ph.D., Forges New Paths in Computational Biology

Written by The Wistar Institute on . Posted in Featured News.

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.

Wistar’s Women and Science Program Talks Melanoma Research

Written by The Wistar Institute on . Posted in Featured News.

After a day of virtual scientific talks that concluded Wistar’s 4th annual Noreen O’Neill Melanoma Research Symposium, a lay-friendly examination of melanoma with a group of interdisciplinary scientists continued into the evening during the Women & Science event Advances in Melanoma and Skin Cancer Research.

Distinguished epidemiologist Dr. Marianne Berwick, from the University of New Mexico, and Wistar Drs. Chengyu Liang, Jessie Villanueva, and Noam Auslander met for a roundtable discussion on melanoma research, prevention, diagnosis, and treatment advances. Dr. Maureen Murphy moderated a lively exchange that touched on the history of melanoma up to the latest solutions to treat and prevent this dangerous skin cancer.

Dr. Berwick kicked off the conversation by addressing why melanoma seems much more prevalent than in the past.

“We wear less clothing, we test for skin cancer with more biopsies, and people spend more time indoors,” says Berwick. “Melanoma incidence increased because we are not covered by our clothes like we were during Victorian times. Also, we have more sensitive detection tools and folks that spend a lot of time indoors then get intermittent but intense sun exposure, increasing the risk of sunburns and developing melanoma.”

Berwick went on to remind the audience of the ABCDs of melanoma and how important it is to know our bodies as any changes in Asymmetry, Border, Color, and Diameter (no wider than a pencil eraser) can be a sign of melanoma.

Cancer researcher Dr. Chengyu Liang spoke of melanoma treatment and why it’s so stubborn to treat.

“For some patients with melanoma, we have different treatments to stimulate their immune system. We can use immunotherapy—finding the wolf (or cancer) in sheep’s clothing, or we can use targeted therapy—finding a way to stop or put on the brakes of an out-of-control car,” says Liang. “Wistar is a front runner in melanoma-targeted therapies and Wistar’s cell bank is vital in the research and treatments that have been accomplished thanks to Dr. Meenhard Herlyn’s lab.”

Dr. Liang joined Wistar less than a year ago and is recognized for her study of melanoma development and progression, with a particular focus on autophagy, or “self-eating”— a process in which cells digest and recycle waste.

“We now can have many patients survive and have their disease controlled through targeted or immunotherapy or a hybrid combo therapy,” said Liang. “But we want 100% survival, and we want to know the right therapy for the right patient at the right time.”

Dr. Jessie Villanueva is a research leader in how tumor cells become resistant. She discussed the challenges of therapy resistance in melanoma—when tumors become indifferent to drugs and escape therapy.

“Some tumors rewire and bypass the effect of the drugs,” says Villanueva. “Sometimes treatment works great for a period, but then tumors become resistant. The genetic make-up of the cancer cells is highly variable within tumors, and even from one another, so drugs can work on some cells but not others. Cancer cells that ‘escape’ treatment can remain asleep and then can be triggered to reawaken, which leads to tumor relapse.”

Dr. Villanueva is developing ways to target NRAS mutations in melanoma.

“The tumors that I work on harbor mutations in NRAS and account for 25-30% of all melanomas,” says Villanueva. “These tumors are highly aggressive and can spread to other organs. NRAS acts as a molecular switch controlling (molecular) signals that instruct the cell to grow or proliferate. A mutation in NRAS breaks the molecular switch, causing cells to proliferate indefinitely and accumulate additional mutations.”

Villanueva continued, “At Wistar, we have the tools and sophisticated models to mimic what happens in a patient’s tumor and we have faculty with diverse skills and backgrounds—from cancer biology, proteomics, and structural biology—to develop novel drugs to combat drug resistant melanoma.”

Dr. Noam Auslander is a computer scientist and uses artificial intelligence to interpret biomedical research data and extract and identify new information. She joined Wistar in June and focuses on the question of who responds to which cancer treatments.

“I do computational work and analyze data sets to generate research questions,” says Auslander. “I build predictors for treatment responses to predict who will respond and who will be resistant. Using these predictors and evaluating large scale data sets for the next drug targets, I hope to find new solutions to drug resistance.”

Before the event ended, the scientists shared challenges or helpful advice they considered key to their success and reminded the attendees to check and protect their skin.

Dr. Noam Auslander

The Wistar Institute Recruits Noam Auslander, Ph.D., as Assistant Professor to Bring Artificial Intelligence Research to Its Cancer Center

Written by The Wistar Institute on . Posted in Press Releases.

PHILADELPHIA — (June 1, 2021) — The Wistar Institute, an international biomedical research leader in cancer, immunology and infectious diseases, announces the appointment of Noam Auslander, Ph.D., as assistant professor in the Molecular and Cellular Oncogenesis Program of The Wistar Institute Cancer Center.

Auslander’s research focuses on the development and application of advanced machine learning methods to investigate cancer progression and evolution of viral infections. Artificial intelligence (AI) uses computing power to process large and complex datasets, integrate different types of data and identify complex patterns in the data. It can uncover biologically and clinically relevant information and help predict prognosis and treatment response.

“We are absolutely thrilled to be able to welcome Noam Auslander to Wistar. Her recruitment is part of our long-range institutional commitment to expand state-of-the-art approaches in computational biology, machine learning and artificial intelligence specifically applied to critical cancer problems,” said Dario Altieri, M.D., Wistar president and CEO, director of The Wistar Institute Cancer Center and the Robert and Penny Fox Distinguished Professor. “Noam has established herself as an emerging leader in these areas, creating innovative algorithms to identify novel genomic predictors of aggressive disease, in particular metastasis, which is responsible for over 90% of all cancer deaths. Our researchers in the Cancer Center cannot be more excited about the broad and impactful collaborations that Noam’s arrival at Wistar will enable, creating new, transformative knowledge to tailor personalized cancer medicine for our patients.”

Auslander is especially interested in how cancer evolves over time. Cancer cells accumulate mutations and other alterations, leading to the emergence of different populations of cells with varying prognoses and metastatic potential. Those that carry the most favorable alterations to promote cancer are selected and cause disease progression. Deciphering this process has important implications for therapy response and resistance to treatment.

“My research is very collaborative by nature, and I’m thrilled by the opportunity to join Wistar’s world class faculty and collaborate with some of the scientists who are advancing transformative cancer research,” said Auslander. “AI has revolutionized other scientific and technologic fields and is starting to show its full potential in biomedical research. At Wistar, it can be used to identify biomarkers, develop clinical predictors, and uncover deleterious alterations. I am looking forward to establishing my laboratory and expanding my research to help answer important biologic questions.”

Auslander majored in computer science and biology at Tel Aviv University, Israel, and received her Ph.D. in computer science from the University of Maryland. She conducted her postdoctoral research work with the Evolutionary Genomics Research group at the National Center for Biotechnology Information of the National Institutes of Health.

###

The Wistar Institute is an international leader in biomedical research with special expertise in cancer research and vaccine development. Founded in 1892 as the first independent nonprofit biomedical research institute in the United States, Wistar has held the prestigious Cancer Center designation from the National Cancer Institute since 1972. The Institute works actively to ensure that research advances move from the laboratory to the clinic as quickly as possible. wistar.org.