IICD Newsletter July 2020

July 08, 2020
July 8th, 2020
Featured Article: Pandemic and
Its Impact on Postdocs and Graduate Students 
In mid-March, the COVID-19 pandemic shut down much of New York City including academic research labs. The three-month-long lockdown that followed has impacted scientific research and brought unique challenges to the research community.

We recently performed a small survey to understand how the postdoctoral researchers and graduate students at our University were holding up. Here are some of the questions we asked.
Q: How has the COVID-19 pandemic impacted you at the personal and/or professional level?
A: Overall, both the postdocs and graduate students felt that the pandemic has affected them deeply, both personally and professionally.
 “This was my first year as a graduate Ph.D. student and therefore I had not established a pipeline or basis of working on my own and on my own projects. I still needed guidance and experience from my colleagues which was hard to get via zoom,” says one student. “I have been unable to go back home to India and have been alone for the past 2.5 months, which has been pretty stressful and mentally challenging. Professionally there was a lot of confusion about third rotations since I’m a first year, and that was definitely stressful,” says Khushboo Kabra. Many other first-year Ph.D. students had similar sentiments. “The third year of Ph.D. is a crucial time for building circles and connections and starting to work with other colleagues within the university or even from other universities. Conferences and workshops provide great opportunities for that and also the social environment in the lab is helpful for starting academic relations,” says Amin Nejatbakhsh. For the students crossing the academic finish line, the dissertation defense was a different experience as it moved online.
  Concerns about families living in a different city or country have been stressful and mentally challenging for many. “I was very stressed about my infected friends here in NY and about my parents and grandparents back in California. Focusing on work has been difficult,” says Aubrianna Decker. Some students with their families abroad are anxious as to when they will be able to see them again safely.
Click here to continue reading the rest of the Q&A
Written by Presha Rajbhandari, Postdoctoral Research Scientist in the Department of Biological Sciences, Brent Stockwell lab
To learn more about COVID-19 view this video narrated by Brent Stockwell.
Meet the IICD Affiliates
Samuel Aparicio, BCh, PhD, FRCPath, FRSC
Sam Aparicio is the Nan & Lorraine Robertson Chair in Breast Cancer Research at the University of British Columbia (UBC) in Vancouver, Canada. He is also Head of the Department of Breast and Molecular Oncology at BC Cancer Research, and a Professor in the Department of Pathology and Laboratory Medicine at UBC. The Aparicio’s lab studies the genomic and phenotypic behavior of breast and other cancers. Integrating leading edge technologies with patient-derived xenograft models of cancer. The lab is also working to develop quantitative measures of clonal fitness in patients, including methods for single cell genome sequencing and PDX models of human cancer. Dr Aparicio recently became Senior Scientific Director of Cancer Genomics at the New York Genome Center and an affiliate member of the Herbert and Florence Institute for Cancer Dynamics. Dr Aparicio is developing a new technology, DLP+, for whole-genome DNA sequencing of single cells. This technology is already present in his lab in Canada and has led to major improvements in the ability to study tumor evolution, by removing many of the artefacts inherent in classical bulk sequencing of tumor DNA. The IICD looks forward to collaborating on DLP+ applications with the New York Genome Center.
Scott Fraser, PhD
Scott E. Fraser is committed to driving forward the convergence between physical and biomedical science. He serves as the Provost Professor of Biology and Bioengineering, the Elizabeth Garrett Professor of Convergent Bioscience, and the Director of Science Initiatives at the University of Southern California. The translation Research Center that Professor Fraser is leading and develops new technologies for the imaging of biological structure and function and provides interdisciplinary training for students, postdocs, and faculty. Fraser has helped found interdisciplinary centers ranging from the Caltech Brain Imaging Center to the Kavli Institute of Nanoscience. As an affiliate member of the Herbert and Florence Irving Institute for Cancer Dynamics, Scott will support the Institute in developing one of its most important research projects, revolving around the understanding of the three-dimensional structure of solid tumors, and the molecular annotation and visualization of cells in situ. Scott will help the Institute set up a serial two-photon tomography system, together with an automated collector, to generate 3D molecular imaging at sub-cellular resolution in complex specimens.
Ben Raphael, PhD
Ben Raphael is a Professor of Computer Science at Princeton University. His research focuses on the design of combinatorial and statistical algorithms for the interpretation of biological data. Recent areas of emphasis include cancer evolution, network/pathway analysis of genetic variants, and structural variation in human and cancer genomes. His group’s algorithms have been used in multiple projects from The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). He co-led the TCGA Pancreatic Adenocarcinoma project and the network analysis in the ICGC Pan-Cancer Analysis of Whole Genomes (PCAWG). Dr Raphael is also an affiliate member of the Herbert and Florence Institute for Cancer dynamics where he will support the mission of the Institute in understanding the dynamics of cancer at different scales:  from cells to patients to populations.
Sohrab Shah, PhD
Sohrab Shah is the Chief of Computational Oncology in the Department of Epidemiology and Biostatistics at the Memorial Sloan Kettering Cancer Center. Dr Shah holds the Nicholls-Biondi Endowed Chair in Computational Oncology at MSKCC. His research focuses on developing and using computational methods to understand cancer evolution and treatment response. At MSKCC, Dr. Shah is building new and innovative capacity in computational methods across the spectrum of data-intensive research activity. This includes multimodal data integration such as genomics and imaging, high-resolution single-cell genomics, and transcriptomics. His translational focus lies in breast cancer and ovarian cancer, in which he has pioneered discovery of prognostic mutational signatures and large-scale studies of mutational landscapes and evolution of these cancers. Dr Shah is an affiliate member of The Herbert and Florence Irving Institute for Cancer Dynamics where he co-mentors with Dr Tavaré a computational biologist, Dr. Vázquez-García. Their collaboration focuses on stochastic models for the evolution of tumors that will be crucial to interpret data generated in the IMAXT Consortium. 
David Tourigny, Ph.D. and Sanket Rane, Ph.D. will join the Herbert and Florence Irving Institute for Cancer Dynamics as Associate Research Scientist on September 1st 2020
David Tourigny, PhD
David Tourigny is currently a Postdoctoral Research Fellow in the Department of Pathology at Columbia University Irving Medical Center. David has an interdisciplinary background in experimental, mathematical, and computational biology. His research interests are the development and application of computational approaches to understand single-cell metabolism, and particularly the role of metabolic heterogeneity in cancer. Specific goals of his current work involve extensions of metabolic modeling, including constraint-based reconstruction and analysis (COBRA) algorithms, to the single-cell regime.
Sanket Rane, PhD
Sanket Rane is currently a Postdoctoral Research Scientist in the Department of Pathology at Columbia University Irving Medical Center. Sanket was trained as an experimental immunologist and over the past 5 years has transitioned into using theoretical approaches to quantify system-level variability in immune interactions. As an Associate Research Scientist, Sanket aims to develop integrative approaches that synthesize deterministic and stochastic mathematical models with experimental data-sets from perturbed and unperturbed systems, and robust statistical methods in order to characterize the collective responses of lymphocyte populations to infections, vaccines, and tumor-antigens.
For more information on our Institute please visit our website at https://cancerdynamics.columbia.edu/
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