Publications

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

  • Sakai, H, Kirino, Y, Kastuma, S, Aoki, F, Suzuki, MG. Morphological and histomorphological structures of testes and ovaries in early developmental stages of the silkworm, Bombyx mori. Journal of Insect Biotechnology and Sericology 2016; 85: 15-20

2015

  • Honda, S, Kirino, Y. SHOT-RNAs: a novel class of tRNA-derived functional RNAs expressed in hormone-dependent cancers. Molecular & Cellular Oncology. 2015;3:2. doi: 10.1080/23723556.2015.1079672.

2014

  • Shigematsu, M, Honda, S, Kirino, Y (2014) "Transfer RNA as a Source of Small Functional RNA"J Mol Biol & Mol Imaging 1(2): 8 doi: Download

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
  • Honda, S and Kirino, Y (2013) “PIWIL1 (piwi-like RNA-mediated gene silencing 1)” Atlas Genet Cytogenet Oncol Haematol. 17(12):833-836. doi: Genes/PIWIL1ID46561ch12q24
  • Pawar K, Kaul G. Toxicity of Europium Oxide Nanoparticles on the Buffalo (Bubalus bubalis) Spermatozoa DNA Damage. Advanced Science, Engineering and Medicine. 5(1):11-17. DOI: https://doi.org/10.1166/asem.2013.1230

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

  • Kirino, Y. and Suzuki, T (2005) "MELAS A3243G mutation and tRNA modification disorder" Rinsyoukensa 49: 89-95

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

Book Chapters

  • Rigoutsos, I and A. Tsirigos, “MicroRNA Target Prediction”. In MicroRNAs in Development and Cancer, F. Slack (Ed.), Imperial College Press, 2010
  • Rigoutsos, I., “Pyknons as putative novel and organism-specific regulatory motifs.” In RNA and the Regulation of Gene Expression, K. Morris (Ed.), Horizon Scientific Press, 2008
  • Rigoutsos, I., D. Platt, A. Califano, and B. D. Silverman, “Representation and matching of small flexible molecules in large databases of 3D-molecular information.” In Pattern Discovery in Molecular Biology, J. Wang, B. Shapiro and D. Shasha (Eds.), Oxford University Press, 1999
  • Rudin, N., K. Inman, G. Stolovitzky and I. Rigoutsos, “DNA-based identification.” In Biometrics: Personal Identification In Networked Society, A. Jain, R. Bolle and S. Pankanti (Eds.), Kluwer Academic Publishers, 1999
  • Silverman, B.D., D. E. Platt, M. Pitman, and I. Rigoutsos, “Comparative molecular moment analysis (CoMMA).” In Perspectives in Drug Discovery and Design, Volumes 12/13/14 3D QSAR in Drug Design: Recent Advances, H. Kubinyi, G. Folkers, and Y.C. Martin (Eds.), Kluwer/Escom, 1998
  • Rigoutsos, I., “Visuo-tactual coarseness estimation tasks: experiments and modeling.” In Advances in Machine Vision: Strategies and Applications, Archibald C. and E. Petriu (Eds.), World Scientific Press, Series in Computer Science – vol. 32, Singapore, July 1992

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