Interests
The amount of high throughput data in biological and clinical systems, from Next Generation Sequencing to Electronic Health Records, is increasing dramatically, allowing the development of a quantitative understanding of complex systems. We are an interdisciplinary team interested in developing and implementing mathematical and computational tools to extract biological and clinical relevant information from large data sets.
Our work is mainly centered around three different topics:
1.- Infectious diseases. Evolution is a dynamical process that shape genomes. Our team at Columbia is developing tools to analyze genomic data, extracting the relevant information to understand the molecular biology, population genetics, evolution, and epidemiology of viruses.
2.- Cancers. Next Generation Sequencing technologies provide an extraordinary opportunity to identify somatic mutations that contribute to the development of tumors. We are developing algorithms to identify driver mutations from high throughput sequence data.
3.- Electronic Health Records. Clinical databases constitute a rich and complex source of high throughput data. We develop and implement statistical methods to extract relevant clinical information and generate medical knowledge.
Publications
Press
Contact information
Raul Rabadan
Department of Biomedical Informatics
Center for Computational Biology and Bioinformatics
Columbia University College of Physicians and Surgeons
1130 St. Nicholas Ave
ICRC Bldg 8th Floor, Office 803B
New York, NY 10032
rabadan[at]dbmi.columbia.edu
People
Raul Rabadan is an Assistant Professor in the Department of Biomedical Informatics and in the Center for Computational Biology and Bioinformatics, at the Columbia University College of Physicians and Surgeons. Dr. Rabadan has been the Martin A. and Helen Chooljian Member at The Simons Center for Systems Biology at the Institute for Advanced Study in Princeton, New Jersey. From 2001 to 2003 he 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. Dr. Rabadan’s current interest focuses on patterns of evolution in biological systems, in particular, RNA viruses.
Vladimir Trifonov received his PhD 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, Princeton, and a year as a research assistant professor at the Department of Mathematics, Statistics, and Computer Science at the University of Illinois, Chicago. His interests in systems biology include models of evolution of micro and macro organisms, and sequencing technologies as applied to whole genome sequencing, association studies, and metagenomic surveys.
Hossein Khiabanian is a Postdoctoral Research Scientist at Department of Biomedical Informatics and Center for Computational Biology and Bioinformatics (C2B2) at Columbia University, working with Prof. Raul Rabadan. Prior to joining Dr. Rabadan’s group, he was a Research Associate and a member of the Observational Cosmology group at Brown University, where he received his Ph.D. in Physics in August 2007. Hossein’s current research interests are in Systems Biology and Computational Virology, especially studying the evolution of viruses.
Benjamin Greenbaum is the Eric and Wendy Schmidt Member of the Simons Center for Systems Biology at the Institute for Advanced Study. Prior to this he spent a year as a postdoctoral fellow in the BioMaPS Institute for Quantitative Biology at Rutgers University. He received his PhD in Physics from Columbia University in 2006. He is currently interested in viral evolution an the host immune system, and how the effects of the evolutionary forces are imprinted in the genome of both pathogen and host.
Joseph Chan is a third-year MSTP student at the Center for Computational Biology and Bioinformatics. He received his B.S. in Biomedical Computation at Stanford University, where he performed research in structural bioinformatics. His projects in this field included analyzing RNA helical coplanarity, automating functional site prediction in protein, and characterizing domain-swapping motifs in proteins. He is currently interested in computational analysis in oncology, virology, and autism.
Oliver Elliott received his B.A. in physics with honors from Amherst College. He worked for a year after graduation on an experiment to measure the electric dipole moment of an electron. He is currently pursuing a master’s in electrical engineering at Columbia and is interested in Next Generation Sequencing Technologies and Systems Biology. Oliver, in collaboration with Vladimir Trifonov, is developing algorithms to search for tumor causing mutations by using high throughput sequencing.
Antony Holmes 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 centre at the University of Warwick to read for his PhD which looked at understanding morphogenesis in myxobacteria. The main interest of Antony are in computational biology, emergent behavior and agent based systems.
Brendan Kelly received his M.D. from Columbia University’s College of Physicians and Surgeons in 2007. He is completing his residency training in the Department of Internal Medicine at New York Presbyterian - Columbia Hospital, and he is planning further training in infectious diseases. His interests include viral evolution, quasispecies, and their implications for vaccine development and drug resistance.
Mrinalini (Mini) Gururaj graduated from Bangalore University in 2007 with a Masters in Biotechnology. As part of master’s thesis, she co-authored a paper on computational drug discovery for alternative herbal remedies for tuberculosis, published in the Journal of Biomolecular Structure and Dynamics. She is currently in the Post Baccalaureate program at Columbia University, pursuing her interest in bioinformatics and computational biology. She is also interested in intellectual property rights issues, regulation in pharmaceutical industry, and oncology.
Jonathan Reichel 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 in New Brunswick, and served in the southern African country of Namibia as a volunteer with the United States Peace Corps, where he taught middle school science and math and learned the Bantu-based Oshindonga language. Currently, Jonathan studies viral evolution, in particular, the recently-discovered XMRV virus.
Past members
Miguel Brown graduated from the University of Rochester in 2004 with a BA in Biology. After graduating, he worked for a year and a half as a lab technician at Ortho-Clinical Diagnostics, a Johnson and Johnson Company. Afterwards, Miguel worked as a lab technician in immunological research lab at the University of Rochester. During my time there, Miguel gained an interest in biomedical informatics - in particular, the bioinformatics side of it. Miguel is now finishing his second year as an MA student here at DBMI and expect to graduate in May of this year (2009).
Alexander Solovyov is a Postdoctoral Research Scientist working jointly in Raul Rabadan lab as well as W Ian Lipkin group at the Center for Infection and Immunity. Prior to joining the group he received his PhD in Physics from Princeton University in 2009. His interests include phylogenetic methods, Next Generation sequencing technologies, evolutionary models and data clustering algorithms as well as their applications to the study of the evolution and discovery of the new viruses.
Philosophy is written in this vast book, which lies continuously open before our eyes (I mean the universe). But it cannot be understood unless you have first learned to understand the language and recognize the characters in which it is written. It is written in the language of mathematics, and the characters are triangles, circles,and other geometrical figures. Without such means, it is impossible for us humans to understand a word of it, and to be without them is to wander around in vain through a dark labyrinth.
(Galileo Galilei, Opere 6:232).
