People

Alumni
Hossein Khiabanian
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Hossein Khiabanian is a professor at Rutgers University. In the Rabadan lab, Hossein's research was in quantitative biology—specifically, developing statistical methods to analyze genomic data, from the study of the molecular epidemiology of disease-causing organisms to investigating the genetics underlying human diseases. He also worked on methods for the early detection of outbreaks, real-time disease surveillance, and analyzing electronic health records. Prior to joining Dr. Rabadan’s group, he was a member of the Observational Cosmology group at Brown University, where he received his Ph.D. in Physics.
h.khiabanian[at]rutgers.edu · homepage

Jiguang Wang
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Jiguang Wang is a professor at The Hong Kong University of Science and Technology. In the Rabadan lab, he worked on cancer evolution and developed computational methods to reveal the evolutionary landscape of tumors under treatment. Jiguang received his Ph.D. in Applied Mathematics from the Academy of Mathematics and Systems Science, where he won the Special Prize of President Scholarship and Excellent PhD thesis Award in the Chinese Academy of Sciences. Prior to working in Dr. Rabadan’s group, he was an assistant research professor at the Beijing Institute of Genomics.
jw2983[at]cumc.columbia.edu · homepage

Francesco Abate
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Francesco Abate currently works at McKinsey & Company. Hereceived his bachelor's and master's degrees at the Polytechnic University of Turin in Italy in 2004 and in 2007, respectively. In 2011 he received his Ph.D. in systems and computer engineering from the Department of Control and Computer Engineering (DAUIN). In 2008 he worked with the CAD Group at the university in the field of fault tolerance and embedded systems and was a visiting student at the Federal University of Rio Grande do Sul (UFRGS) in Porto Alegre, Brazil. In 2009 he joined the Polytechnic University of Turin's Electronic Design Automation Group. In the Rabadan Lab, he worked on the design of data mining tools applied to bioinformatics, the development of next generation sequencing analysis pipelines, and computational biology problems in cancer.

Daniel Scholes Rosenbloom
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Daniel Scholes Rosenbloom currently works at Merck. He received his Ph.D. in Organismic and Evolutionary Biology from Harvard University in 2013. As a member of the Program for Evolutionary Dynamics at Harvard, he focused on mathematical models of viral infection and evolution. Together with the Rabadan Lab, Daniel is currently developing methods in “topological genomics” — using tools from algebraic topology to characterize both human evolution and the spread of HIV. He also collaborates with the Siliciano Lab at Johns Hopkins Medical School on issues of HIV treatment and latency.
daniel.rosenbloom[at]gmail.com · homepage

Pablo G. Camara
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Pablo G. Camara is an Assistant Professor at the University of Pennsylvania. He is currently interested in the application of topological techniques to the study of recombination in organisms, with particular emphasis on human genetics. He received his Ph.D. in Theoretical Physics in 2006 and performed research in High Energy Physics between 2006 and 2014, with postdoctoral appointments at Ecole Polytechnique, the European Organization for Nuclear Research (CERN), and University of Barcelona.
pg2495[at]columbia.edu

Joseph Chan
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Joseph Chan is a medical resident at Weill Cornell Medical Center. He received his B.S. in Biomedical Computation at Stanford University and graduated from the Columbia University MSTP program in 2014 with an MD and PhD in computational biology. His PhD dissertation, under the mentorship of Dr. Rabadan, focused on developing novel techniques in algebraic and network topology of influenza evolution. In particular, he modeled the global spread of seasonal influenza as a network that predicted the importance of different nodes (locations) in the transmission of the virus. He also developed a novel method based on algebraic topology that captured clonal and reticulate evolution in viruses. The second half of his thesis focused on cancer—in particular, the detection of gene fusions in glioblastoma, which led to the discovery of targetable, recurrent FGFR-TACC and EGFR-SEPT14 fusions.

Michael Lesnick
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Michael Lesnick is postdoctoral fellow at the Institute for Mathematics and its Applications in Minneapolis. He visited the Rabadan Lab in 2015. In 2012, he received his Ph.D. from Stanford University in computational mathematics. In 2012-2013, he was a Member of The School of Mathematics at the Institute for Advanced Study, and since then has been at the IMA. Michael's research focuses on topological data analysis; he is interested in theoretical foundations, development of new tools for exploratory data analysis, and applications to biology.
mlesnick[at]ima.umn.edu

Rachel Melamed
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Rachel Melamed is currently a postdoctoral researcher in the Rzhetsky Lab at The University of Chicago. She received her Ph.D. from the Department of Biomedical Informatics at Columbia in 2015. Her undergraduate concentration was in computer science at Brown University. After a stint in software engineering, Rachel worked as a research assistant at the Benoist-Mathis Lab at Harvard Medical School, where she analyzed microarray data to understand mechanisms of T-cell activation as well as to compare mouse models of autoimmune disease. She has also worked on understanding cell signaling in immune cell types, and in immune-derived cancer cells, using many-dimensional single cell cytometric measurements.

Albert Lee
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Albert Lee was a Ph.D. student in the Department of Biomedical Informatics. He received his B.S. in molecular, cell, and developmental biology with honors from the University of California at Los Angeles. In 2013, he received his master's in Biomedical Informatics. His research interest centers on the statistical analysis of RNA sequencing data to elucidate the transcriptomes of uncharacterized species. He has also worked on problems in cancer and infectious disease.

Kevin Emmett
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Kevin Emmett received his Ph.D. in the Rabadan Lab. His research interests are applications of topological data analysis to genomic data and the statistical topology of models in population genetics. Areas of focus include population structure and human demographic models, lateral gene transfer in bacteria and viruses, and statistical models of chromatin spatial organization. Additional work has involved machine learning methods for predicting host adaptation in infectious diseases, statistical models for analyzing next generation sequencing data, and signaling network inference in cancer. Kevin was jointly advised by Chris Wiggins.
kje2109[at]columbia.edu

Sakellarios Zairis
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Sakellarios Zairis is an MD/PhD student at Columbia with a background in physics and biomedical engineering. His current work focuses on using machine learning approaches to understand how oncogenic viruses affect the mutational landscape of certain cancers. Sakellarios is a member of the Wiggins Lab.
siz2102[at]columbia.edu

Ohad Balaga
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Ohad Balaga received his bachelor's degree in Computer Science and Computational Biology from The Hebrew University of Jerusalem. His research at HUJI revolved around combinatorial gene regulation by microRNA and the inference of such regulation from gene expression and network data. In the Rabadan Lab, Ohad's research focused on influenza mutations, evolution and quasispecies. He worked jointly with Dr. Sagi Shapira.

Patrick van Nieuwenhuizen
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Patrick is an MD student at Columbia University College of Physicians and Surgeons. He graduated from Princeton University in 2010 with an A.B. in Physics. After graduation he spent two years in Zimbabwe building Upenyu Health Group, a non-profit devoted to treating parasitic worm infections. He is interested in applying topological data analysis to oncology and other aspects of medicine.
phv2105[at]cumc.columbia.edu

Udi Rubin
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Udi Rubin received his B.S.c in Natural Sciences from the Open University of Israel in 2013. Working for several years in the Israeli Hi-Tech scene alongside his growing passion for the life sciences, led him to pursue Columbia’s M.A Biotechnology degree. In his master’s thesis, Udi applies topological data analysis techniques on bulk and single-cell RNA-seq data to study non-small cell lung cancer.
uer2102[at]columbia.edu

Efua Peterson
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Efua Peterson is an undergraduate at Columbia University pursuing a B.A. in mathematics as a pre-medical student. She is interested in genomics and oncology, and in Rabadan Lab she is applying methods of topological data analysis to the study of genetic recombination.
eop2103[at]columbia.edu

Bryan Hisashi Louie
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Bryan is a third year undergraduate at Columbia University pursuing a B.S. in Biomedical Engineering. He previously worked in the Cell and Molecular Biomechanics Lab at Columbia, where he studied the mechanotransduction pathway of primary cilia in bone. His current interests are in cancer biology and genomics. In the Rabadan Lab, he is currently working on a project on cancer evolution.
bhl2118[at]columbia.edu

Jacqueline Aw
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Jacqueline is undertaking a summer observership at the Rabadan Lab. She is a third year undergraduate majoring in Biochemistry and Cell Biology, at the Hong Kong University of Science and Technology. She is interested in elucidating lncRNA shuttling mechanisms based on sequence homology.
jtmaw[at]connect.ust.hk

Jonathan Reichel
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Jonathan Reichel is currently lead bioinformatics scientist at the Innovation Laboratory in the Center for Molecular Oncology at Memorial Sloan Kettering Cancer Center. He graduated with high honors in Biological Sciences from the University of Maryland in College Park, where he worked on a human genetics association study and designed paramagnetic nanotubes made from silicon dioxide and magnetite for use in bioextraction and future drug delivery systems. Since then, he has studied computer engineering as a post-baccalaureate student at Rutgers University and served in the Peace Corps. In the Rabadan Lab, Jonathan worked on developing computational tools to discover signals in high-throughput sequencing data with a focus on cancer, gene fusions, and novel pathogens.
jbr95[at]cornell.edu

Alex Penson
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Alex Penson is a senior computational biologist at Memorial Sloan Kettering. In the Rabadan Lab, his research focused on searching for traces of disease-causing organisms in genetic data as well as studying the molecular basis of Myelodysplastic syndrome and Hodgkin’s lymphoma. He worked on computational and statistical methods to efficiently analyze large amounts of genomic data, drawing on skills honed during his doctoral work in high energy physics searching for hypothetical sub-atomic particles called gravitons at the LHC in Switzerland.

Zachary Carpenter
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Zachary Carpenter currently works at McKinsey & Company. He received a Ph.D from the Columbia Department of Pharmacology and Molecular Signaling in 2014. He was also a fellow of the Med into Grad Scholars (MIG) Program at Columbia University's College of Physicians and Surgeons. He graduated from the College of New Jersey in 2009 with a B.S. in biology and minors in chemistry and computer science. His participation in the MIG Scholars program at Columbia enabled him to obtain medical experience in pediatric and adult hematological oncology, which was his main research focus under Dr. Rabadan and Dr. Adolfo Ferrando. He also studied structure-based drug design, in silico pharmacology, and clonal evolution and phasing in cancer.

Vladimir Trifonov
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Vladimir Trifonov is a research scientist at The Genomics Institute of the Novartis Research Foundation (GNF), in San Diego. He received his Ph.D. in computer science from the University of Texas at Austin in 2006. He spent a year as a postdoctoral fellow at the School of Mathematics at the Institute for Advanced Study in Princeton, and a year as a research assistant professor in the Department of Mathematics, Statistics, and Computer Science at the University of Illinois, Chicago.

Benjamin Greenbaum
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Benjamin Greenbaum is an assistant professor in the department of Medicine, Hematology and Medical Oncology at Mount Sinai. Previously , he was the Eric and Wendy Schmidt Member of the Simons Center for Systems Biology at the Institute for Advanced Study in Princeton. Prior to this, he spent a year as a postdoctoral fellow in the BioMaPS Institute for Quantitative Biology at Rutgers University. He received his Ph.D. in Physics from Columbia University in 2006.
benjamin.greenbaum[at]mssm.edu

Eric Minwei
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Eric Minwei Liu is currently a PhD student at Weill Cornell Medical College. He holds a master’s degree from the Department of Biomedical Informatics at Columbia University, where he received the 2012 Mitsubishi UFJ Trust Scholarship. He graduated from National Taiwan University in 2005 with a dual B.S. degree in chemistry and information management and in 2007 with an M.S. degree in pharmaceutical science. After graduation, he continued working at NTU in the Jung-Hsin Lin Lab, where he built activated structure models of adenosine A2A and designed potential ligands for treating Huntington’s disease by conducting simulations of molecular dynamics.

Antony Holmes
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Antony Holmes is a postdoctoral research scientist in the lab of Riccardo dalla Favera at Columbia University. He studied computer science at the University of Warwick in the UK between 2000 and 2004. During this time he also undertook several internships at Unilever Research where he worked in the bioinformatics department on database projects to manage patient data. In 2005 he moved to a newly opened interdisciplinary research center at the University of Warwick to read for his Ph.D. which looked at understanding morphogenesis in myxobacteria.
antony.holmes[at]dbmi.columbia.edu

Carlos Hernández
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Carlos Hernández is pursuing his Ph.D. at Stanford University. He graduated from Columbia University's School of Engineering and Applied Science, where he studied Applied Mathematics with a concentration in quantitative biology. His research interests include the molecular epidemiology of viruses and oncoviral discovery. In the past, he has worked on discerning the swine-origin of A/H1N1 human influenza pandemic using Bayesian analysisi and pathogen discovery in sequencing data. He has been awarded both Genentech and HHMI fellowships to work in the labs of Stephen Goff and Andrew McCammon, respectively.
cxh[at]stanford.edu · homepage

Alex Hawson
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Alex Hawson is an anesthesiology resident at University of Rochester Medical Center. He graduated from Columbia University College of Physicians and Surgeons in 2012 and magna cum laude from Columbia University with a B.A. in Economics. Prior to medical school, Alex worked as a senior consultant at Deloitte focused on medical management and pharmaceutical pricing regulatory compliance. After Deloitte, he worked as a consultant developing custom software for hedge funds. Alex did a year of research in the Rabadan Lab applying data mining techniques to identify new associations for rare diseases.

Tamar Sery
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Tamar Sery Amster is a software engineer at Bloomberg. She received her B.Sc. in Chemistry and Computer Science from Hebrew University in Jerusalem. She worked as a programmer in the Roichman lab at Tel Aviv University, applying image-processing techniques to study the process of wetting of surfaces. Later she worked in the Yitzchaik lab (Hebrew University), applying experimental polymerization and hydrosilylation techniques, as part of a team trying to develop better solar cells. In the Rabadan Lab, Tamar worked on a machine-learning project trying to predict drug sensitivity based on genomic and pharmaceutical data.

Judith Kribelbauer
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Judith Kribelbauer is a PhD student in the Integrated Program (C2B2 track) at Columbia. In 2012, she received her bachelor degree in Chemistry from the University of Heidelberg with a focus in theoretical and biological chemistry. Before starting the PhD-program at Columbia, she did a research year in Dr. Weeks lab at UNC-Chapel Hill working on structural alterations of HIV-RNA using next-generation sequencing.
jfk2132[at]columbia.edu

Santiago Vilar
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Santiago Vilar received his Ph.D. from the Laboratory of Pharmaceutical Chemistry at the University of Santiago de Compostela, Spain, in 2006. The following year, he was awarded a grant to work in molecular docking at the University of Padova, Italy. In 2008 Santiago began a two-year postdoctoral fellowship working in the Laboratory of Biological Modeling at the National Institutes of Health (NIH) in Bethesda, Maryland. His research interests span different methodologies in computational chemistry, such as QSAR/QSPR in small molecules and proteins, and molecular modeling applied to structure-based drug discovery and explanations of biomolecular mechanisms of action.

Miguel Brown
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Miguel Brown is a bioinformatics programmer at The University of Chicago School of Medicine. He graduated from the University of Rochester in 2004 with a B.A. in biology. He has worked as a researcher at the University of Rochester, Ortho-Clinical Diagnostics, the Rabadan Lab, and the Tuschl Lab at Rockefeller University.

Alexander Solovyov
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Alexander Solovyov is postdoctoral fellow at the Icahn School of Medicine at Mount Sinai. Previously, he was an Associate Research Scientist working in the Ian Lipkin group at the Center for Infection and Immunity and the NorthEast Biodefense Institute. He received his Ph.D. in physics from Princeton University in 2009. His interests include phylogenetic methods, next generation sequencing technologies, evolutionary models and data clustering algorithms as they apply to the study of the evolution and the discovery of new viruses.

Kripa Sivakumar
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Kripa Sivakumar is software engineer at Amazon. He received a master's degree in the Department of Computer Science at Columbia University. In the Rabadan Lab, he collaborated with Joseph Chan on identifying somatic mutations related to tumor progression. In particular, he worked on inflammatory breast cancer, glioblastoma multiforme and melanoma.

Brendan Kelly
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Brendan Kelly is currently a practicing physician. He received his M.D. from the Columbia University College of Physicians and Surgeons in 2007. He completed his residency in the Department of Internal Medicine at New York Presbyterian Hospital and did a fellowship at the University of Pennsylvania.

Mrinalini Gururaj
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Mrinalini "Mini" Gururaj graduated from Bangalore University in 2007 with a master's in biotechnology. As part of her master’s thesis, she co-authored a paper on computational drug discovery for alternative herbal remedies for tuberculosis, which was published in the Journal of Biomolecular Structure and Dynamics. In 2011 she got her master's from Columbia University in biotechnology. Her master's thesis was entitled "DNA Transfection Methods for Mammalian Cells."

Richard Wolff
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Richard Wolff is a rising senior at Columbia College majoring in mathematics with a concentration in computer science. He goes by Ricky, and in his free time enjoys playing the guitar. He hopes one day to use his background in pure math to approach problems in medicine in new and fundamental ways.

Samuel Resnick
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Sam Resnick is an MD/PhD student at Columbia University College of Physicians and Surgeons. He graduated with a BS in Biology from the University of North Carolina at Chapel Hill in 2015. Previously, he studied how different chromatin remodeling complexes impact transcriptional regulation and contribute to tumorigenesis.

Kyle Bolo
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Kyle graduated from Williams College in 2013 with a B.A. in mathematics. For two years, after graduating, he worked on software for Emergency Departments and coordinated a support team as a technical engineer at Epic, the electronic health record company. He is currently an MD student at Columbia University's College of Physicians and Surgeons. He investigates intra-host HIV recombination using topological data analysis.

David Gu
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David is a second-year M.D. student at Columbia University College of Physicians and Surgeons. He graduated from Columbia University in 2012 with a B.S. in Operations Research, and he spent several years working in finance prior to matriculation. His current interests are in genomics and cancer evolution.
yg2206[at]cumc.columbia.edu

Nikhil Bommakanti
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Nikhil is an MD student at Columbia University College of Physicians and Surgeons. He graduated from the University of Illinois at Chicago with a BS in Bioengineering then deferred entry to P&S to spend one year at the University of Oxford on a Whitaker Fellow Grant. Nikhil is working on a project on long noncoding RNA in pancreatic cancer with the support of an NIH T35 training grant.

Zikai Wu
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Zikai Wu is a visiting associate research scientist, studying precision medicine in the Department of Biomedical Informatics at Columbia University. He received his Ph.D. in Operations Research and Cybernetics from Dalian University of Technology, China. He is an associate professor of University of Shanghai for Science and Technology, China. His current work is focusing on developing computational methods to study gene-drug interaction. Zikai joined Dr. Rabadan's group in September 2016.
zw2416[at]cumc.columbia.edu

Ian Huang
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Ian is an undergraduate student at Columbia University, double majoring in computer science and financial economics. His past research has been focused on machine learning applied to the classification of heart transplant rejection severity within medical images. Now he is working on finding the relationship between noncoding and coding RNA genes in pancreatic cancer. He is also part of the Columbia Organization of Rising Entrepreneurs (CORE) and the Columbia University Medical Informatics Society, and enjoys playing violin and watching Netflix in his free time.
iyh2110[at]columbia.edu

Pingzhang Wang
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Pingzhang Wang is a visiting associate research scientist. In 2011, he received his Ph.D. in Immunology from the Department of Immunology, Peking Univerity Health Science Center. He is also an associate professor of the department. His research interest focuses on omic big data-driven knowledge discovery (BD2K) in immunology and cancer fields. In Jan. 2017, Pingzhang joined Dr. Rabadan's group. Currently, he works on multiple omic data mining to address gene regulatory mechanisms in immune cells, and also in cancers.
pingzhangwang[at]gmail.com