People

Principal Investigator
Raul Rabadan
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Raul Rabadan is a Professor in the Department of Systems Biology and Biomedical Informatics at Columbia University. He is the director of the Center for Topology of Cancer Evolution and Heterogeneity. From 2001 to 2003, Dr. Rabadan was a fellow at the Theoretical Physics Division at CERN, the European Organization for Nuclear Research, in Geneva, Switzerland. In 2003 he joined the Physics Group of the School of Natural Sciences at the Institute for Advanced Study. Previously, Dr. Rabadan was the Martin A. and Helen Chooljian Member at The Simons Center for Systems Biology at the Institute for Advanced Study in Princeton, New Jersey. He has been named one of Popular Science's Brilliant 10 (2010), a Stewart Trust Fellow (2013), and he received the Harold and Golden Lamport Award at Columbia University (2014). Dr. Rabadan’s current interest focuses on uncovering patterns of evolution in biological systems—in particular, RNA viruses and cancer.

Executive Director
Sophie Thuault-Restituito
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Sophie Thuault-Restituito received her doctorate in pharmacy and her PhD in neuroscience from the University of Montpellier, France. She later completed a postdoc in the laboratory of Steve Moss at University College London, and then worked as a research associate scientist and research assistant professor in the Department of Biochemistry and later in the Department of Neuroscience and Physiology at the New York University Langone Medical Center. She moved to an administrative position at NYU in 2013 and became research operation manager for the Medical Science Building and then director of research laboratory operation and utilization at Langone. As executive director and scientific operation manager for the Columbia University Center for Topology of Cancer Evolution and Heterogeneity, Sophie combines her expertise in experimental biology and management to oversee the administration of the Physical Sciences-Oncology center and other NIH- and foundation-supported grants.
st3090[at]cumc.columbia.edu

Postdoctoral Researchers
Zhaoqi Liu
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Zhaoqi Liu is a postdoctoral research scientist, studying cancer genomics in the Department of Biomedical Informatics at Columbia University. He received his Ph.D. in Applied Mathematics from the Academy of Mathematics and Systems Science, where he won the President's Scholarship prize. Zhaoqi joined Dr. Rabadan’s group in September 2015. His current work focuses on developing computational methods to analyze biological problems in cancer genomics.
zl2495[at]cumc.columbia.edu

Mykola Bordyuh
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Mykola Bordyuh is a postdoctoral research scientist in the Department of Biomedical Informatics. He received his B.S. and M.S. degrees from the Moscow Institute of Physics and Technology in Applied Mathematics and Physics and his Ph.D. in Electrical Engineering from Princeton University. His current research interests are applications of topological data analysis to biological data with an emphasis on cancer genomics.

Junfei Zhao
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Junfei Zhao is a postdoctoral research scientist, studying cancer genomics in the Department of Biomedical Informatics at Columbia University. His current work is focusing on developing computational methods to study biological problems in cancer genomics. He received his Ph.D. in Applied Mathematics from University of Chinese Academy of Sciences. Junfei joined Dr. Rabadan's group in September 2016.
jz2835[at]cumc.columbia.edu

Ioan Filip
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Ioan Filip is a postdoctoral research scientist in the Department of Biomedical Informatics. He received his Ph.D. in Mathematics from Columbia University in 2016. As a member of the Rabadan Lab, Ioan is currently studying the genetic basis of the immune response to viral infections and he is interested in further developing algebraic and topological methods to model evolution.
ioan.filip[at]gmail.com

Luis Aparicio
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Luis Aparicio is a postdoctoral research scientist in the laboratory of Raul Rabadan. He did his graduate degree in Physics combined with studies in Mathematics at Universidad Autonoma in Madrid and Music at the Conservatory specializing in harpsichord and ancient music. He received his M.Sc. and PhD in Theoretical Physics at the Institute for Theoretical Physics in Madrid. He did his first postdoctoral research at the International Centre for Theoretical Physics (Trieste) working at the interface between String Theory, Particle Physics and Cosmology. His current research interest is focused on developing mathematical methods to address problems in Systems Biology with special emphasis in applying topological techniques in the contexts of single-cell and cancer genomics.
luisapariciods[at]gmail.com

Juan Angel Patiño-Galindo
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Juan Angel Patiño-Galindo is a postdoctoral research scientist, working on virus evolution in the Department of Systems Biology. His PhD focused on studying different aspects of the mid- and long-term evolution of RNA viruses, with special interest in molecular epidemiology of HIV and HCV. His current research involves the application of topological and phylogenetic methods to the analysis of viral evolution.
jp3770[at]cumc.columbia.edu

Wesley Tansey
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Wesley Tansey is a postdoctoral research scientist in the Department of Systems Biology. He received his Ph.D. in Computer Science from the University of Texas at Austin in 2017 with a focus on machine learning and computational statistics. Wesley's work in the Rabadan lab revolves around leveraging latent structure in biological data to develop more powerful analysis tools for cancer. His projects include dose-response prediction for cancer treatments, single cell RNA-Seq denoising, and spatial modeling of tumor samples.
wes.tansey[at]gmail.com

Francesco Brundu
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Francesco G. Brundu is a Post-Doctoral Research Scientist in the Department of Systems Biology. He received his B.S., M.S. and Ph.D. from the Polytechnic University of Turin. During his Ph.D., he collaborated with the Candiolo Cancer Research Institute and the Academical Medical Center of Amsterdam, with specific focus on the stratification of Colorectal Cancer through gene expression and copy number variation analysis. His current research interests focus on i) the analysis of genomic variation through computational tools and ii) the application of single-cell RNA sequencing to Cancer Genomics.
francesco.brundu[at]gmail.com

Mathieu Carriere
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Mathieu Carrière is a postdoctoral research scientist in the Department of Systems Biology. He received his PhD in Informatics from Inria and Université Paris Saclay in 2017. He is interested in the application of Topological Data Analysis in Machine Learning frameworks, with an emphasis on biological data. He is currently working on bootstrap methods for Mapper complexes computed on gene expression data, as well as predictive analysis of single cell Hi-C contact maps through persistence diagrams.
mc4660[at]cumc.columbia.edu

Doctoral Students
Andrew Chen
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Andrew Chen is an MD/PhD student at Columbia University rotating with the Rabadan lab. He graduated with a B.S. in Physics from MIT in 2015. His undergraduate work was in population dynamics, as well as researching combination therapeutic design at Takeda Pharmaceuticals. He is interested in applying computational methods to cancer evolution

Karen Gomez
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Karen Gomez is an MD/PhD student at Columbia University College of Physicians and Surgeons. She graduated from Temple University with a B.S. in Biochemistry in 2017. Her undergraduate research focused on studying cancer evolution through tumor phylogenetics. Currently, she is investigating associations between genetic data and phenotype as well as clinical outcomes in cancer. She is interested in cancer genomics.
kg2726[at]cumc.columbia.edu

Staff
Oliver Elliott
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Oliver Elliott received his B.A. from Amherst College and his M.S. from Columbia University. In the Rabadan Lab, Oliver has worked on pathogen discovery in high throughput sequencing data, transcriptome annotation, and identifying somatic variants in cancer. He is an all-purpose programmer and works on a mix of web development, bioinformatics programming, and sysadmin.
oe2118[at]cumc.columbia.edu

Tim Chu
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Tim received his B.A. in biology at NYU in 2012 and his Masters' in computer science at NYU in 2016. Previously, he worked in a microbiology lab studying the spore coat of B. subtilis. Currently, his work is focused on pipeline design and data visualization.
tc2813[at]cumc.columbia.edu

Janelle Nunez
Janelle Nunez is the administrator and lab manager for the Rabadan Lab. Please direct inquiries about the lab to her.
jn2531[at]columbia.edu

Master's Students
Kernyu Park
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Kernyu Park is currently an MA candidate in the department of biomedical informatics (DBMI) at Columbia. He received his BA in Biology from Columbia University in 2016. He has worked on cleaning genome variant data of cancer patients to better predict the correlation between the variants and cancer genes and is now interested in translational analysis of NGS whole genome sequencing data for infectious diseases.
kernyu.park[at]columbia.edu

Undergraduates
Monika Francsics
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Monika is an undergraduate at Columbia University pursuing a B.A. in computer science and mathematics. She is interested in algebraic topology and big data analytics techniques. At the Rabadan Lab, she is studying bacterial and viral interactions in the human microbiome and their role in infection using topological data analysis.
mf3145[at]columbia.edu

Rose Orenbuch
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Rose Orenbuch is a senior at Columbia University, where she is majoring in Information Science with a concentration in biology and neuroscience. She is investigating associations between genetics and immune response during viral infections, using genomic data. Furthermore, she is developing an application for genotyping highly polymorphic regions using standard RNA sequencing reads.
rose.orenbuch[at]columbia.edu