Director of Computational Medicine Center, Professor in the Department of Pathology, Anatomy and Cell Biology, Department of Biochemistry & Molecular Biology, Department of Cancer Biology and member of the Kimmel Cancer Center Isidore Rigoutsos

Director of Computational Medicine Center, Professor in the Department of Pathology, Anatomy and Cell Biology, Department of Biochemistry & Molecular Biology, Department of Cancer Biology and member of the Kimmel Cancer Center

Short Bio

Dr. Rigoutsos is the Director of the Computational Medicine Center at Thomas Jefferson University (TJU). He joined TJU in early 2010 as a Professor with an appointment in the Department of Pathology, Anatomy & Cell Biology. He also has joint appointments in the Department of Cancer Biology, and the Department of Biochemistry & Molecular Biology, and is a member of the Kimmel Cancer Center at TJU. For nearly 18 years prior to joining TJU, Dr. Rigoutsos was with IBM's Thomas J. Watson Research Center where he founded and managed the Bioinformatics and Pattern Discovery group. In parallel to his IBM tenure, Dr. Rigoutsos was for a decade a Visiting Lecturer at MIT's Dept. of Chemical Engineering where he taught graduate-level classes and summer professional courses in Bioinformatics. Dr. Rigoutsos’ involvement in the field of Computational Biology spans the last nearly twenty years. During this time, he has been developing computer algorithms for studying genomic architecture and analyzing very large biological datasets. Since 1996, his efforts have revolved around the theoretical and practical aspects of pattern discovery and the design of pattern-based solutions to a variety of problems from genomics, genetics, molecular biology and medicine. Starting in 2002, Dr. Rigoutsos’ work placed particular emphasis on the study of non-coding RNAs (microRNAs, pyknons, piRNAs, etc.). Of particular interest are the questions surrounding the biogenesis of such non-coding RNAs, the mechanisms of action and the automated discovery of their targets, the discovery of novel organism-specific regulatory sequences, and the elucidation of the roles of non-coding RNAs in the onset and progression of disease. Some of Dr. Rigoutsos earlier work revolved around the solving of partial differential equations in 2 and 3 dimensions, using the adaptive mesh refinement method.  An interesting problem which arises in that context is that of embedding grid points (where the solution needs further refinement) in rectangles in a manner that minimizes the computational effort that is needed to improve the solution at those points. Joint work with Marsha Berger led to the development of a very efficient gridding scheme, now known as the Berger-Rigoutsos algorithm, for solving the problem. This picture, from a shock impacting an inclined slope, shows how the algorithm places rectangles at those locations that require a better-quality solution. A graduate of the Physics Dept. of the National and Kapodistrian University of Athens, Greece, Dr. Rigoutsos received a Master’s in Computer Science from the University of Rochester, and a Master’s and Doctoral degrees in Computer Science from New York University’s Courant Institute of Mathematical Sciences.

Publications

Papers

 

2017

  • Magee, R, Telonis, AG, Cherlin, T, Rigoutsos, I, Londin, E. Assessment of isomiR Discrimination Using Commercial qPCR Methods. Non-Coding RNA 2017, 3(2), 18; doi:10.3390/ncrna3020018.

2016

2015

2014

2013

  • Loher, P, Vasilakis, N, Malamon, J, Chen, HW and Rigoutsos, I (2013) "HandsFree - Next Generation Sequence Processing, Mapping and Analysis Made Easy" Proceedings DILS2013 doi: DILS-SYS-EC-paper4

2012

2011

2010

  • Huynh, T., M. Vlachos and I. Rigoutsos. (2010) "Anchoring millions of distinct reads on the human genome within seconds" Proceedings 13th International Conference on Extending Database Technology (EDBT), Lausanne, Switzerland

2009

2008

2007

2006

2005

2004

  • Rigoutsos, I. and T. Huynh "Chung-Kwei: a pattern-discovery-based system for the automatic identification of unsolicited e-mail messages (SPAM)" First Conference on Email and Anti-Spam (CEAS2004), Mountain View, CA, July 2004
  • Moxley, J., G. Stephanopoulos and I. Rigoutsos "Systems biology: using systems approaches to manage biological complexity" Foundations of Computer Aided Process Design Conference on Discovery though Product and Process Design (FOCAPD 2004), Princeton University, Princeton, NJ, July 2004

2003

2002

  • Wang, X., J. T.L. Wang, D. Shasha, B. A. Shapiro, I. Rigoutsos and K. Zhang "Finding patterns in three dimensional graphs: algorithms and applications to scientific data mining" IEEE Transactions on Data and Knowledge Engineering 14(4):731-749, July/August 2002

2001

  • Platt, D. E., L. Parida, Y. Gao, A. Floratos and I. Rigoutsos "QSAR in grossly underdetermined systems: opportunities and issues" IBM Journal of Research and Development 45(3/4):533-544, May/July 2001
  • Floratos, A., I. Rigoutsos, L. Parida and Y. Gao "DELPHI: a pattern-based method for detecting sequence similarity" IBM Journal of Research and Development 45(3/4):455-474, May/July 2001
  • Parida, L., I. Rigoutsos and D. E. Platt "An output-sensitive flexible pattern discovery algorithm" Proceedings 12th Annual Symposium on Combinatorial Pattern Matching (CPM 2001) pp. 131-142, Jerusalem, Israel, July 2001

Before 2000

  • Parida, L., I. Rigoutsos, A. Floratos, D. Platt, and Y. Gao "Pattern discovery on character sets and real valued data: linear bound on irredundant motifs and an efficient polynomial time algorithm" Proceedings 11th Annual ACM/SIAM Symposium on Discrete Algorithms (SODA '00), pp. 297-308, San Francisco, CA, January 2000
  • Floratos, A., I. Rigoutsos, L. Parida, G. Stolovitzky and Y. Gao "Sequence homology detection through large-scale pattern discovery" Proceedings 3rd Annual ACM International Conference on Computational Molecular Biology (RECOMB '99) pp. 164-173, Lyon, France, April 1999
  • Parida, L., A. Floratos and I. Rigoutsos "An approximation algorithm for alignment of multiple sequences using motif discovery" Journal of Combinatorial Optimization 3(2/3):247-275, July 1999
  • Rigoutsos, I., A. Floratos, C. Ouzounis and Y. Gao "From motif discovery to functional characterization and structure prediction: a feasible journey" Proceedings 2nd Annual TIGR Conference on Computational Genomics Reston, VA. November 1998
  • Rigoutsos, I. and A. Delis "Managing statistical behavior of large data sets in networked architectures" IEEE Transactions on Parallel and Distributed Systems 9(11):1073-1087, November 1998
  • Rigoutsos, I. and A. Floratos "Motif discovery without alignment or enumeration" Proceedings 2nd Annual ACM International Conference on Computational Molecular Biology (RECOMB '98) pp. 221-227, New York, NY, March 1998
  • Rigoutsos, I "Well-behaved, tunable 3D affine invariants" Proceedings IEEE Conference on Computer Vision and Pattern Recognition (CVPR '98) Santa Barbara, CA. June 1998
  • Rigoutsos, I "2D affine-invariants that distribute uniformly and can be tuned to any convex feature domain" Proceedings International Conference on Computer Vision (ICCV '98) Bombay, India, January 1998
  • Wang X., J. Wang, D. Shasha, B. Shapiro, S. Dikshitulu, I. Rigoutsos and K. Zhang "Automated discovery of active motifs in three dimensional molecules" Proceedings 3rd International Conference On Knowledge Discovery And Data Mining (KDD-97) Newport Beach, CA, August 1997
  • Wolfson, H. and I. Rigoutsos "Geometric Hashing: an overview" IEEE Computational Science & Engineering 4(4):10-21, October-December 1997
  • Rigoutsos, I. and A. Delis "The impact of hashing function choice on the load balancing in very large datasets" Proceedings 8th International Conference on Software Engineering and Knowledge Engineering (SEKE '96) Lake Tahoe, NE. June 1996
  • Rigoutsos, I. and R. Hummel "A Bayesian approach to model matching with geometric hashing" Computer Vision and Image Understanding 62(1):11-26, July 1995
  • Rigoutsos, I. and A. Califano "dFLASH: a distributed fast look-up algorithm for string homology" Proceedings Conference on Parallel Computation and Problem Solving Environments Dartmouth Institute for Advanced Graduate Studies, Hanover, NH, July 1994
  • Rigoutsos I. and A. Califano "Searching in parallel for similar strings" IEEE Computational Science and Engineering 1(2):60-75, Summer 1994
  • Rigoutsos, I. and R. Hummel "Distributed Bayesian object recognition" Proceedings IEEE Conference on Computer Vision and Pattern Recognition (CVPR '93) New York, NY, June 1993
  • Califano, A. and I. Rigoutsos "FLASH: a fast look-up algorithm for string homology" Proceedings IEEE Conference on Computer Vision and Pattern Recognition (CVPR '93) New York, NY. June 1993
  • Rigoutsos, I. and R. Hummel "Massively parallel model matching: geometric hashing on the connection machine" IEEE Computer: Special Issue on Parallel Processing for Computer Vision and Image Understanding 25(2):33-42, February 1992
  • Berger, M. and I. Rigoutsos "An algorithm for point clustering and grid generation" IEEE Transactions on Systems, Man and Cybernetics 21(5):1278-1286, September/October 1991
  • Rigoutsos, I. and R. Hummel "Several results on affine geometric hashing" Proceedings 8th Israeli Conference on Artificial Intelligence and Computer Vision Tel Aviv, Israel. December 1991
  • Rigoutsos, I. and R. Hummel "Robust similarity invariant matching in the presence of noise" Proceedings 8th Israeli Conference on Artificial Intelligence and Computer Vision Tel Aviv, Israel. December 1991
  • Rigoutsos, I "Visuo-tactual coarseness estimation tasks: 1: experiments, 2: modeling" Proceedings Vision Interface ’91, Calgary, Canada, June 1991
  • Rigoutsos, I. and R. Hummel "Implementation of geometric hashing on the connection machine" Proceedings IEEE Workshop on Directions in Automated CAD-Based Vision Systems, Maui, Hawaii. June 1991
  • Aloimonos, J., and I. Rigoutsos "Detection of 3D motion without correspondence; planar surfaces: theory and experiments, curved surfaces: theory" Proceedings AAAI-86 Philadelphia, PA. August 1986
  • Aloimonos, J. and I. Rigoutsos "How to determine structure, depth and 3D motion of a textured plane, without correspondence" Proceedings Canadian Artificial Intelligence ‘86 Montreal, Canada. May 1986
  • Aloimonos, J. and I. Rigoutsos "Determining the 3D motion of a rigid planar patch without correspondence, under perspective projection" Proceedings IEEE Workshop on Motion Charleston, SC. May 1986

Books/BookChapters

 

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Contact Info