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Research Publications

Please contact me or use scholar.google.com to get copies of the papers below

    Book Chapters

  1. Graph Model of Coalescence with Recombinations,
    Author: Laxmi Parida
    The Problem Solving Handbook for Computational Biology and Bioinformatics (Lecture notes in mathematics)
    Editors: Lenwood S. Heath, Naren Ramakrishnan
    Publisher: Springer Verlag, 2010.

  2. Discovering patterns in gene order,
    Authors: Laxmi Parida and Niina Haiminen
    Evolutionary genomics: statistical and computational methods
    Editor: Maria Anisimova (Series editor: John Walker)
    Methods in Molecular Biology, 2012, Volume 855, Part 3, 431-455, DOI: 10.1007/978-1-61779-582-4_16.
    Publisher: Springer Humana.

  3. Non-redundant Representation of Ancestral Recombinations Graphs,
    Author: Laxmi Parida
    Evolutionary genomics: statistical and computational methods
    Editor: Maria Anisimova (Series editor: John Walker)
    Methods in Molecular Biology, 2012, Volume 856, Part 3, 315-332.
    Publisher: Springer Humana.

    4. Modeling/Algorithmics

  4. Javed, A., Pybus, M., Melè, M., Utro, F., Bertranpetit, J., Calafell, F., and Parida, L., IRiS: Construction of ARG networks at genomic scales, vol 27, Issue 17, Pp. 2448-2450 Bioinformatics, 2011.
  5. Recombination networks as genetic markers: a human variation study of the Old World, Javed, A., Melè, M., Pybus, M., Zalloua, P., Haber, M., Comas, D., Netea, M., Balanovsky, O., Balanovska, E., Jin, L., Yang, Y., Arunkumar G., Pitchappan, R.M., Bertranpetit, J., Calafell, F., Parida, L., and The Genographic Consortium, Human Genetics, 2011
  6. The footprint of recombination gives a new insight in the effective population size and the history of the Old World human populations, Melè, M., Javed, A., Pybus, M., Zalloua, P., Haber, M., Comas, D., Netea, M., Balanovsky, O., Balanovska, E., Jin, L., Yang, Y., Pitchappan, R.M., Arunkumar G., Parida, L., Calafell, F., Bertranpetit J., and The Genographic Consortium, Molecular Biology and Evolution, 2011
  7. Characterizing and Extracting Irredundant Tandem Motifs, Laxmi Parida, Cinzia Pizzi, and Simona E. Rombo, under submission, 2011.
  8. Experiences with Mining Temporal Event Sequences from Electronic Medical Records: Initial Successes and Some Challenges, Debprakash Patnaik, Patrick Butler, Naren Ramakrishnan, Laxmi Parida, Benjamin J. Keller, David A. Hanauer, The 17th ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD-2011), 2011.
    Mining Significant Partial Order Patterns in Electronic Medical Records, to be presented at the Annual Symposium of AMIA (American Medical Informatics Association), Oct 22-26, Washington, DC, 2011.
  9. Pooled BAC Sub-Genome Sequencing QTL-rich Region of the Theobroma cacao Genome, F. Alex Feltus, Chris A. Saski, Keithanne Mockaitis, Niina Haiminen, Laxmi Parida, Zachary M. Smith, James B. Ford, Margaret E. Staton, Stephen P. Ficklin, Barbara P. Blackmon, Ray J. Schnell, David N. Kuhn , Juan-Carlos Motamayor, BMC Genomics, 2011.
  10. A Minimal Descriptor of an Ancestral Recombinations Graph, Laxmi Parida, Pier Francesco Palamara, Asif Javed, BMC Bioinformatics, 2011, 12(Suppl 1):S6doi:10.1186/1471-2105-12-S1-S6
  11. Assessing Pooled BAC and Whole Genome Shotgun Strategies for Complex Genome Assembly, Niina Haiminen, F. Alex Feltus, Laxmi Parida, BMC Genomics, 2011.
  12. A Protocol and Benchmarks for Evaluating Methods of de novo Genome Assembly from High-throughput Sequencing Reads, Niina Haiminen, David Kuhn, Laxmi Parida, Isidore Rigoutsos, PLoS one, 2011.
  13. A New Method to Reconstruct Recombination Events at a Genomic Scale, Marta Mele, Asif Javed, Francesc Calafell, Laxmi Parida, Jaume Bertranpetit, PLoS Computational Biology 2010.
    Oral presentations of the results at the following meetings: GENOME INFORMATICS, Cold Spring Harbor Laboratory, New York, October 27 - 30, 2009, and Molecular Anthropology in the Genomic Era, 4th International conference of the series DNA polymorphisms in human populations, Rome, December 3 - 5, 2009.
  14. Recombinomics: Population Genomics from a Recombination Perspective, Asif Javed, Laxmi Parida, Proceedings of C3S2E, Montreal, 2010.
  15. Combinatorics in Recombinational Population Genomics, Laxmi Parida, ISBRA 2010, LNBI 6053, pp. 126--127, 2010 (Keynote Abstract).
  16. Ancestral Recombinations Graph: A Reconstructability Perspective using Random-Graphs Framework, Laxmi Parida, Journal of Computational Biology, 2010.
  17. VARUN: Discovering Extensible Motifs under Saturation Constraints, Alberto Apostolico, Matteo Comin, Laxmi Parida, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, no. 4, pp. 752-762, Oct.-Dec. 2010, doi:10.1109/TCBB.2008.123.
  18. Minimizing Recombinations in Consensus Networks for Phylogeographic Studies, Laxmi Parida, Asif Javed, Marta Mele, Francesc Calafell, Jaume Bertranpetit, BMC Bioinformatics , APBC, Beijing, 2009.
  19. A case for Recombinomics, Laxmi Parida, Asif Javed, Marta Mele, Jaume Bertranpetit, IBM Technical Report RC24677, August, 2008.
  20. Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns, Laxmi Parida, Marta Mele, Francesc Calafell, Jaume Bertranpetit and The Genographic Consortium, Journal of Computational Biology, vol 15, No 9, pp 1--22, 2008.
  21. Detection of Subtle Variations as Consensus Motifs, Matteo Comin, Laxmi Parida, Theoretical Computer Science, 395(2-3), pp 158-170, May, 2008.
  22. Exploring the Recombinant Genome for Phylogeography: Algorithms for Inferring Deep Ancestry, Parida L., Mele M., Calafell F., Bertranpetit J. and Genographic Consortium, International Genetic Congress, Berlin, July 12-17, 2008.
  23. Statistical Significance of Large Gene Clusters, Laxmi Parida, Journal of Computational Biology, 14(9), pp 1145--1159, 2007.
  24. Gapped Permutation Pattern Discovery for Gene Order Comparisons, Laxmi Parida, Journal of Computational Biology, vol 14, No 1, pp 46-56, 2007.
  25. Using PQ Structures for Genomic Rearrangement Phylogeny, Laxmi Parida, Journal of Computational Biology, 13(10), pp 1685-1700, 2006
  26. Subtle Motif Discovery for Detection of DNA regulatory sites, Matteo Comin, Laxmi Parida, Series on Advances in Bioinformatics and Computational Biology, as proceedings of Asia Pacific Bioinformatics Conference (APBC2007), vol 5, Hong Kong, pp 27--36, Jan 14-17, 2007.
  27. Automatic Discovery of Gapped Permutation Patterns with Size Constraints, Laxmi Parida, Dagstuhl Proceedings of Series 06201 Combinatorial and Algorithmic Foundations of Pattern and Association Discovery, May 15-20, 2006.
  28. Motif Patterns in 2D, Alberto Apostolico, Laxmi Parida, Simona E. Rombo, Theoretical Computer Science, vol 390, N0 1, pp 40-55, 22 January 2008.
  29. PROTERAN: Animated Terrain Evolution for Visual Analysis of Patterns in Protein Folding Trajectory, Ruhong Zhou, Laxmi Parida, Kush Kapila, Sudhir Mudur, vol 23, No 1, Bioinformatics, pp 99--106, 2007.
  30. Constructing Near-Perfect Phylogenies with Multiple Homoplasy Events R V Satya, A Mukherji, G Alexe, L Parida, G Bhanot, ISMB, Bioinformatics, 514-522, 2006.
  31. Using Permutation Patterns for Content-Based Phylogeny, Enam Karim, Laxmi Parida, Arun Lakhotia, Pattern Recognition in Bioinformatics, LNBI 4146, pp 115-125, 2006.
  32. Modeling the Combinatorial Control of Transcription using Partial Order Motifs and their Redescriptions, Naren Ramakrishnan and Laxmi Parida, under submission 2006.
  33. Gapped Permutation Patterns for Comparative Genomics, Laxmi Parida, Proceedings of WABI, Algorithms in Bioinformatics, LNBI 4175, pp 376-387, 2006.
  34. A PQ Framework for Reconstructions of Common Ancestors & Phylogeny Laxmi Parida, Proceedings of RECOMB-CG, Comparative Genomics, LNBI 4205, pp 141-155, 2006.
  35. Clustering, Patterns, Trees and Common Origins: An Analysis of Complete mtDNA Sequences, G Bhanot, G Alexe, D Platt, R Vijayasatya, L Parida, S Rosset, A Royyuru, RECOMB 2006 poster.
  36. Discovering Topological Motifs Using a Compact Notation, Laxmi Parida, Journal of Computational Biology, 14(3), pp 46--69, 2007.
  37. Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a $\beta$-hairpin, L Parida, R Zhou, PLoS Computational Biology, vol 1:1, June 2005.
  38. Mining, Compressing and Classifying with Extensible Motifs, A. Apostolico, M. Comin, L. Parida, , 2005.
  39. Gene Proximity Analysis Across Whole Genomes via PQ Trees, G M Landau, L Parida, O Weimann, Journal of Computational Biology, 12(10), pp 1289--1306, 2005.
  40. Malware Phylogeny Generation Using Permutations of Code, M E Karim, A Walenstein, A Lakhotia, L Parida, Journal in Computer Virology, 2005.
  41. Redescriptions: Strucutre Theory & Algorithms, Laxmi Parida, Naren Ramakrishnan, AAAI 2005, Pittsburgh, pp 837-844, July 9-13, 2005.
  42. Using PQ Trees for Comparative Genomics, G M Landau, L Parida, O Weimann, CPM 2005 Jeju Island, South Korea, LNCS 3537 Springer 2005, ISBN 3-540-26201-6, pp 128-143, June 19-21, 2005. abstract.
  43. Malware Phylogeny Using Maximal pi-Patterns, Arun Lakhotia, Md Enamul Karim, Andrew Walenstein, Laxmi Parida, EICAR 2005, Malta, April 30-May 3, 2005.
  44. Off-line Compression by Extensible Motifs, A. Apostolico, M. Comin, L. Parida, Data Compression Conference (DCC), Snowbird, Utah, March 29-31, 2005.
  45. Conservative Extraction of Over-represented Motifs, A. Apostolico, M. Comin, L. Parida, ISMB 2005 Michigan, pp 9-18, June 25-29, 2005. abstract, PDF.
  46. Protein Folding Trajectory Analysis using Patterned Clusters, J Feng, L Parida, R Zhou, Series on Advances in Bioinformatics and Computational Biology, as proceedings of Asia Pacific Bioinformatics Conference (APBC2005), vol 3, Singapore, pp 95--104, Jan 17-21, 2005.
  47. Motifs in Ziv-Lempel-Welch Clef, A. Apostolico, M. Comin, L. Parida, IEEE Proceedings of Data Compression Conference (DCC), Snowbird, Utah, pp 72--81, March 23-25, 2004.
  48. Permutation Pattern Discovery in Biosequences, R Eres, G M Landau, L Parida, Journal of Computational Biology, vol 11, No 6, pp 1050-1060, 2004.
  49. Incremental Paradigms of Motif Discovery, Alberto Apostolico, Laxmi Parida, Journal of Computational Biology, vol 11, No 1, pp 15-25, 2004.
  50. An inexact suffix tree based algorithm for extensible pattern discovery, Abhijit Chattaraj, Laxmi Parida, Theoretical Computer Science, 335:1, pp 3-14, 2005.
  51. Bridging Lossy and Lossless Compression by Motif Pattern Discovery, A. Apostolico, M. Comin, L. Parida, General Theory of Information Transfer and Combinatorics, Vol II, (editors R Ahlswede, L Baumer, N Cai), 2004.
  52. A Combinatorial Approach to Automatic Discovery of Cluster Patterns, Revital Eres, Gad M Landau, Laxmi Parida, Proceedings of WABI 2003, LNBI vol 2812, pp 139--150, September 15-20, 2003. ( conference photos by Tetsuo)
  53. The Web Server of IBM's Bioinformatics and Pattern Discovery Group, Tien Huynh, Isidore Rigoutsos, Laxmi Parida, Daniel Platt, Tetsuo Shibuya, Nuleic Acids Research, 31(13):3645-3650, July 2003.
  54. Developing a similarity measure in biological function space, Ronald Jensen, Haiyuan Yu, Laxmi Parida, Gustavo Stolovitzky, Mark Gerstein, 2003.
  55. Compression and the Wheel of Fortune, Alberto Apostolico, Laxmi Parida, IEEE Proceedings of Data Compression Conference (DCC), Snowbird, Utah, pp 143--152, March 25-27, 2003. Work also presented at LSD 03, ( London Stringology Day 03 ), King's College, London, February 26, 2003.
  56. Dictionary-driven Protein Annotation, Isidore Rigoutsos, Tien Huynh, Aris Floratos, Laxmi Parida, Daniel Platt, Nucleic Acid Research, 2002, Vol 30 No 17 3901--3916.
  57. TeiresiasP: Parallelized Data Mining for Shared and Distributed Environments, Tien Huynh, Laxmi Parida, Daniel Platt, Isidore Rigoutsos, under submission, 2002.
  58. In Silico Pattern-based Analysis of the Human Cytomegalovirus (HHV5) Genome, Isidore Rigoutsos, Jiri Novotny, Tien Huynh, Stephen Chin-Bow, Laxmi P. Parida, Daniel E. Platt, David Coleman, Thomas Shenk, RC22551, Watson Research Report (W0208-078), August 28, 2002. Also in Journal of Virology, 2003.
  59. An Output-sensitive Flexible Pattern Discovery Algorithm, Laxmi Parida, Isidore Rigoutsos, Dan Platt, Combinatorial Pattern Matching ( CPM 2001 ), LNCS vol 2089, pp 131--142, 2001. (conference photos by Anne , by Leszek )
  60. DELPHI: A Pattern-based Method for Detecting Sequence Similarity, Aris Floratos, Isidore Rigoutsos, Laxmi Parida, Yuan Gao, IBM Journal of Research and Development, vol 45, Number 3/4, pp 455--474, May/July 2001.
  61. QSAR in Grossly Underdetermined Systems: Opportunities and Issues , Daniel Platt, Laxmi Parida, Yuan Gao, Isidore Rigoutsos, IBM Journal of Research and Development, vol 45, Number 3/4, pp 533--544, May/July 2001.
  62. Some Results on Flexible-pattern Discovery, Laxmi Parida, Combinatorial Pattern Matching (CPM 2000), LNCS vol 1848, pp 33--45, 2000.
  63. Pattern Discovery on character sets and real-valued data: linear bound on irredundant motifs and polynomial time algorithms, Laxmi Parida, Isidore Rigoutsos, Aris Floratos, Dan Platt, Yuan Gao, Proceedings of the eleventh ACM-SIAM Symposium on Discrete Algorithms (SODA 2000), January 2000, pp 297--308.
  64. Building Dictionaries of 1D and 3D Motifs by Mining the Unaligned 1D Sequences of 17 Archaeal and Bacterial Genomes, Isidore Rigoutsos, Yuan Gao, Aris Floratos, and Laxmi Parida, Proc. of the Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB 99), Heidelberg, August 6-10, 1999, pp 223--233.
  65. The Emergence of Pattern Discovery Techniques in Computational Biology, Isidore Rigoutsos, Aris Floratos, Laxmi Parida, Yuan Gao, and Daniel Platt, Journal of Metabolic Engineering , 2(3):159-177, July 2000.
  66. Sequence Homology Detection Through Large-Scale Pattern Discovery, Aris Floratos, Isidore Rigoutsos, Laxmi Parida, Gustavo Stolovitzky and Yuan Gao, Proc. of the ACM Conference on Computational Molecular Biology (RECOMB 99), Lyon, April 11-14, 1999, pp 164--173. (Download figures)
  67. Dictionary Building Via Unsupervised Hierarchical Motif Discovery In The Sequence Space of Natural Proteins Isidore Rigoutsos, Aris Floratos, Christos Ouzounis, Yuan Gao, Laxmi Parida, Proteins: Structure, Function and Genetics, 37(2):264-277, 1999.
  68. MUSCA: An Algorithm for Constrained Alignment of Multiple Data Sequences, Laxmi Parida, Aris Floratos and Isidore Rigoutsos, Genome Informatics 1998, No 9, 112-119, Universal Academy Press, 1998.
  69. An Approximation Algorithm for Alignment of Mulitple Sequences using Motif Discovery, Laxmi Parida, Aris Floratos and Isidore Rigoutsos, Journal of Combinatorial Optimization, Vol 3 No 2/3, August 1999, pp 247--275.

    70. Population genomics

    (as Genographic Consortium)
  70. Influences of history, geography, and religion on genetic structure: the Maronites in Lebanon. Haber M, Platt DE, Badro DA, Xue Y, El-Sibai M, Bonab MA, Youhanna SC, Saade S, Soria-Hernanz DF, Royyuru A, Wells RS, Tyler-Smith C, Zalloua PA; The Genographic Consortium. Eur J Hum Genet. 19:333-40 (2011).
  71. Ancient DNA from European early neolithic farmers reveals their near eastern affinities. Haak W, Balanovsky O, Sanchez JJ, Koshel S, Zaporozhchenko V, Adler CJ, Der Sarkissian CS, Brandt G, Schwarz C, Nicklisch N, Dresely V, Fritsch B, Balanovska E, Villems R, Meller H, Alt KW, Cooper A; and Members of The Genographic Consortium. PLoS Biol. 8:e1000536 (2010).
  72. A mitochondrial revelation of early human migrations to the Tibetan Plateau before and after the last glacial maximum. Qin Z, Yang Y, Kang L, Yan S, Cho K, Cai X, Lu Y, Zheng H, Zhu D, Fei D, Li S, Jin L, Li H; and The Genographic Consortium. Am J Phys Anthropol. 143:555-69 (2010).
  73. Genetic heritage and native identity of the Seaconke Wampanoag tribe of Massachusetts. Zhadanov SI, Dulik MC, Markley M, Jennings GW, Gaieski JB, Elias G, Schurr TG; Genographic Project Consortium. Am J Phys Anthropol. 142:579-89 (2010).
  74. Geographical structure of the Y-chromosomal genetic landscape of the Levant: a coastal-inland contrast. El-Sibai M, Platt DE, Haber M, Xue Y, Youhanna SC, Wells RS, Izaabel H, Sanyoura MF, Harmanani H, Bonab MA, Behbehani J, Hashwa F, Tyler-Smith C, Zalloua PA; Genographic Consortium. Ann Hum Genet. 73:568-81 (2009).
  75. Identifying genetic traces of historical expansions: Phoenician footprints in the Mediterranean. Zalloua PA, Platt DE, El Sibai M, Khalife J, Makhoul N, Haber M, Xue Y, Izaabel H, Bosch E, Adams SM, Arroyo E, López-Parra AM, Aler M, Picornell A, Ramon M, Jobling MA, Comas D, Bertranpetit J, Wells RS, Tyler-Smith C; Genographic Consortium. Am J Hum Genet. 83:633-42 (2008).
  76. Maximum-likelihood estimation of site-specific mutation rates in human mitochondrial DNA from partial phylogenetic classification. Rosset S, Wells RS, Soria-Hernanz DF, Tyler-Smith C, Royyuru AK, Behar DM; Genographic Consortium. Genetics 180:1511-24 (2008).
  77. A novel 154-bp deletion in the human mitochondrial DNA control region in healthy individuals. Behar DM, Blue-Smith J, Soria-Hernanz DF, Tzur S, Hadid Y, Bormans C, Moen A, Tyler-Smith C, Quintana-Murci L, Wells RS; Genographic Consortium. Hum Mutat 29:1387-91 (2008).
  78. The dawn of human matrilineal diversity. Behar DM, Villems R, Soodyall H, Blue-Smith J, Pereira L, Metspalu E, Scozzari R, Makkan H, Tzur S, Comas D, Bertranpetit J, Quintana-Murci L, Tyler-Smith C, Wells RS, Rosset S; Genographic Consortium. Am J Hum Genet. 82:1130-40 (2008).
  79. Y-chromosomal diversity in Lebanon is structured by recent historical events. Zalloua PA, Xue Y, Khalife J, Makhoul N, Debiane L, Platt DE, Royyuru AK, Herrera RJ, Hernanz DF, Blue-Smith J, Wells RS, Comas D, Bertranpetit J, Tyler-Smith C; Genographic Consortium. Am J Hum Genet. 82:873-82 (2008).
  80. The Genographic Project public participation mitochondrial DNA database. Behar DM, Rosset S, Blue-Smith J, Balanovsky O, Tzur S, Comas D, Mitchell RJ, Quintana-Murci L, Tyler-Smith C, Wells RS; Genographic Consortium. PLoS Genet. 3:1083-1095 (2007).

    81. Single Molecule Methods

  81. Partitioning Single Molecule Maps into Multiple Populations: Algorithms and Probabilistic Analysis, Laxmi Parida, Bud Mishra, Discrete Applied Mathematics (The Computational Molecular Biology Series) , vol 104, pp 203-227, 2000.
  82. Partitioning K Clones: Hardness Results and Practical Algorithms for the K-Populations Problem, Laxmi Parida, Bud Mishra, Proc. of the ACM Conference on Computational Molecular Biology (RECOMB 98), 192-201, New York, March 1998.
  83. Algorithmic Complexity of Physical Mapping Problems Arising in Single Molecule Methods, Laxmi Parida, IBM Technical Report, 1998.
  84. On the Approximability of Physical Map Problems using Single Molecule Methods Laxmi Parida, Proceedings of Discrete Mathematics and Theoretical Computer Science (DMTCS 99), pp 310-328, Auckland, January 1999.
    Inapproximability of Flip-Cut, Shift-Cut and other problems from Optical Mapping, Laxmi Parida, Courant Inst. of Math. Sciences, NYU, TR1997-740, August 1997.
  85. Mass Estimation of DNA Molecules & Extraction of Ordered Restriction Maps in Optical Mapping Imagery, Laxmi Parida, Davi Geiger, Algorithmica, special issue on Computational Biology, vol 25. No 2/3, October-November, pp 295-310, 1999.
  86. A Uniform Framework for Ordered Restriction Map Problems , Laxmi Parida, Journal of Computational Biology, Vol 5, No 4, Mary Ann Liebert Inc Publishers, pp 725--739, (winter) 1998.
  87. Towards Constructing Physical Maps by Optical Mapping: An Effective, Simple, Combinatorial Approach , S. Muthukrishnan, Laxmi Parida, Proc. of the First ACM Conference on Computational Molecular Biology (RECOMB 97), 209-219, Santa Fe, January 1997.
  88. A Model and Solution to the DNA Flipping String Problem, Davi Geiger, Laxmi Parida, Courant Inst. of Math. Sciences, NYU, TR1996-720, May 1996.
  89. The Disk-Covering Method for Tree Reconstruction, Daniel Huson, Scott Nettles, Laxmi Parida, Tandy Warnow and Shibu Yooseph, Algorithms and Experiments (Alex 98), Trento, February 1998.
  90. Computational Molecular Biology: A Survey of Problems and Tools , Laxmi Parida, Journal of the Indian Institute of Science (Special Issue on Computational Biology), vol 77, pp 283--326, July-August, 1997.

    91. Thesis

  91. Algorithmic Techniques in Computational Genomics, Laxmi Parida, PhD thesis, Courant Institute of Mathematical Sciences, New York University, September 1998.

    (This thesis received the Janet Fabri Award for an outstanding thesis in computer science, Courant Institute, 1999. Some earlier parts of the work received the Sandra Bleistein Award for notable achievement by a woman in applied mathematics and computer science, Courant Institute, 1996.)

    92. Computer Vision

  92. Junctions: Detection, Classification and Reconstruction , Laxmi Parida, Davi Geiger, Robert Hummel, IEEE Transactions on Pattern Analysis and Machine Intelligence (PAMI), vol 20, No 7, July 1998, pp 687--698 .
  93. Kona: A Multi-Junction Detector Using Minimum Description Length Principle , Laxmi Parida, Davi Geiger, Robert Hummel, Energy Minimization Methods in Computer Vision and Pattern Recognition (EMMCVPR'97), Marcello Pelillo, Edwin Hancock (Eds), LNCS vol 1223, pp 51-65, May 1997.
  94. Visual Organization for Figure/Ground Separation , Davi Geiger, Krishnan Kumaran, Laxmi Parida, Proc. of Computer Vision and Pattern Recognition (CVPR 96), San Francisco, pp 155-160, 1996.
  95. Feature Transform for ATR Image Decomposition, Signal Processing, Sensory Fusion, and, Target Recognition IV, Davi Geiger, Robert Hummel, Barney Baldwin, Tyng-Luh Liu, Laxmi Parida, The International Society for Optical Engineering (SPIE) Proceedings Vol 2484, Orlando, 1995, pp 512-523.

    96. Geometric Computing

  96. Common Tangents to Two Planar Parametric Curves: A Geometric Solution, Laxmi Parida, S.P. Mudur, Vol 27, No. 1, Computer-Aided Design, pp. 41-47, January, 1995.
  97. Computational Methods for Evaluating Swept Object Boundaries, Laxmi Parida, S.P. Mudur, 10:266-276, The Visual Computer, 1994.
  98. Constraint-satisfying Planar Development of Complex Surfaces, Laxmi Parida, S.P. Mudur, Vol 25, No. 4, Computer-Aided Design, pp. 225-232, April, 1993.
    (Nine pages of Figures appear separately     here .)
  99. Vinyas: An Interactive Calligraphic Type Design System, Laxmi Parida, Proc. of the International Conference on Computer Graphics (ICCG 93), North-Holland Publishing, pp. 355-368, February 1993.
    (Two pages of Figures appear separately     here .)
  100. A Computational Technique for General Shape Deformations for use in Font Design, Laxmi Parida, Vol 17, No. 4, Computers & Graphics, pp. 349-356, 1993.
  101. A Closed Form Solution to the Problem of Tangential Circles, Lines, Points with extension to 3D, Laxmi Parida, Pramod Koparkar, Vol 15, No. 1, Computers & Graphics, pp. 49-55, 1991.
    (Three pages of Figures appear separately     here .)

    102. Social Software

  102. Sock Sorting, Laxmi Parida, Rohit Parikh, Vaughan Pratt, editors Jelle Gerbrandy, Maarten Marx, Maarten de Rijke and Yde Venema, JFAK. Essays Dedicated to Johan van Benthem on the Occasion of his 50th Birthday , Amsterdam University Press, Vossiuspers, Amsterdam, 1999, ISBN 90 5629 104 1.
  103. Sock Sorting: An Example of a Vague Algorithm, Rohit Parikh, Laxmi Parida, Vaughan Pratt, Logic Journal of the IGPL, Vol 9, Issue 5: September 2001.

Patent Activities

Please use the United States Patent & Trademark Office (USPTO) databases to download full text of the following.

  1. SAMPLING THE SPACE OF ANCESTRAL RECOMBINATION GRAPHS, U.S. Serial No. 13/169,824, June 27, 2011
  2. Significance Measure of Structured Clusters, US Patent 7925447, April 12, 2011.
  3. SYSTEM AND METHOD FOR IDENTIFYING A GAPPED PERMUTATION PATTERN, US Patent 7917305, March 29, 2011
  4. METHOD AND SYSTEM FOR COMPARATIVE GENOMICS, US Patent 7881874, Feb 1, 2011
  5. Assembly Error Detection, U.S. Serial No. 13/010949, Jan 21, 2011
  6. Methods and Systems for conservative extraction of over-represented extensible motifs, US Patent 7,865,313, Jan 4, 2011
  7. Pattern Discovery Techniques for Determining Maximal Irredundant and Redundant Motifs, USPTO 20100057373, March 04, 2010.
  8. METHOD AND SYSTEM FOR IDENTIFYING PARTIAL ORDER PATTERNS IN SEQUENCES OF DATA, USPTO 20090259626, Oct 15, 2009.
  9. Topological Motif Discovery, US Patent 7,558,768, July 7, 2009.
  10. METHOD FOR RECONSTRUCTING EVOLUTIONARY DATA, USPTO 20090132584, May 21, 2009.
  11. Apparatus, system and method for data compression using irredundant patterns, US Patent 7,479,905, Jan 20, 2009.
  12. OBJECT CLASSIFICATION USING AN OPTIMIZED BOOLEAN EXPRESSION, U.S. Patent 7428515, Sep 23, 2008.
  13. VISUAL ANALYSIS OF A PROTEIN FOLDING PROCESS, USPTO 20080183452, July 31, 2008.
  14. METHOD AND APPARATUS FOR DETECTING CONSENSUS MOTIFS IN DATA SEQUENCES, USPTO 20080167850, July 10, 2008.
  15. Methods and systems for reconstructing genomic common ancestors, USPTO 20080167850, Jan 31, 2008.
  16. Method and system for clustering objects and finding prime redescriptors for the clusters, USPTO 0070213957, Sept 13, 2007.
  17. Method and structure for lossy compression of continuous data with extensible motifs, U.S. Patent 7259701, August 21, 2007.
  18. System and Method for Encoding and Detecting Extensible Patterns, U.S. Patent 7203680, April 10, 2007.
  19. Method and system for protein folding trajectory analysis using patterned clusters, USPTO 20060069515, March 30, 2006.
  20. Fuzzy bi-clusters on multi-feature data, USPTO 20060184459, Aug 17, 2006.
  21. Discovering Permutation Patterns, USPTO 20050060321, March 17, 2005.
  22. Methods and Apparatus for Performing Pattern Discovery and Generation with respect to Data Sequences, U.S. Patent 6571230, May 27, 2003.
  23. Multiple Sequence Alignment System and Method, U.S. Patent 6205444B1, March 20, 2001.

Invited Talks

(See conference publications for papers presented at conferences)

  1. Recombination-based genomics: a genetic variation analysis in human populations, Albert Einstein College of Medicine, Bronx, Sept 21, 2011.
  2. Recombination-based genomics: a genetic variation analysis in populations, Indiana University, Bloomington, Sept 15, 2011.
  3. The Re-combinatorics of Chromosomes, Computer Science Colloquia, Purdue University, West Lafayette, Sept 13, 2011.
  4. Entropy of a standard ARG is not very high!, Parc de Recerca Biomedica de Barcelona (PRBB), Barcelona, Spain, Feb 23, 2011.
  5. The Cacao Genome Project, (with Niina Haiminen) PAG XIX, San Diego, Jan 15-19, 2011.
  6. Beyond SNPs: Influence of Genetic Recombinations on Population Structures, Genomics & Genomic Medicine, Lee Gil Ya Cancer and Diabetes Institute, Gachon University of Medicine and Science, Incheon, Jan 13, 2011.
  7. Random Graphs and Population Genetics, Seoul National University, Seoul, Jan 10, 2011.
  8. The Re-Combinatorics of Diploids, Columbia University, Oct 20, 2010.
  9. The Re-Combinatorics of Diploids, CCMB Distinguished Lecture Series, Brown University, Sept 29, 2010.
  10. How robust are NGS whole-genome assemblies? A case study with plant genomes, (with Niina Haiminen) ECCB, Ghent, Belgium, Sept 28, 2010.
  11. Combinatorics of Recombinations in Diploids, NCBI/NIH, Bethesda, July 30, 2010.
  12. Combinatorics In Recombinational Population Genomics, , keynote at ISBRA, Storrs, May 23-26, 2010.
  13. Recombinomics: Phylogenetic approach to genome-wide analysis in populations, , keynote at C* Conference on Computer Science & Software Engineering (C3S2E), Montreal, May 19-20, 2010.
  14. Graph Theory in Recombinational Population Genomics, keynote at APBC (Asia Pacific Bioinformatics Conference) Bangalore, Jan 18-22, 2010.
  15. Graph Theoretic Approaches to RECOMBINOMICS, keynote at Robert Cedergren Bioinformatics Colloquium, Université de Montreal, Nov 5-6, 2009.
  16. Graph Theory in Recombinational Population Genomics, CSE Colloquium Series, UCONN, Oct 12, 2009.
  17. RECOMBINOMICS: myth or reality ? DIMACS Workshop on Algorithmics in Human Population-Genomics, April 27--29, 2009.
  18. Combinatorial-Statistic of Genes, Department of Computer Science, Princeton University, Princeton, Feb 19, 2009.
  19. Informatics in Bioinformatics, keynote address at International Symposium on Role of IT Professionals in Bioinformatics, Regional College of Management (RCM), Bhubaneswar, Jan 7, 2009.
  20. Deep Computing in Biology, National Institute of Science Education and Research (NISER), Bhubaneswar, Jan 6, 2009.
  21. Modeling Statistical Significance of Gene Clusters, Supercomputer Education and Research Centre (SERC), Indian Institute of Science (IISc), Bangalore, Dec 30, 2008.
  22. A Case for Recombinomics, Strand Life Sciences, Bangalore, Dec 30, 2008.
  23. RECOMBINOMICS: myth or reality ?National Centre for Biological Sciences (NCBS), Bangalore, Dec 29, 2008.
  24. Mathematical Models in Recombinomics, University of Delhi, International Congress of Mathematics, New Delhi, Dec 19-20, 2008.
  25. Algorithmics in Recombinational Phylogeography, IBM T J Watson, Hawthorne, Dec 08, 2008.
  26. Algorithms in Population Genetics, NYU Women in Computing, IBM T J Watson, Nov 14, 2008.
  27. Combinatorial Statistics of Gene Clusters, Mathematical & Computational Biology Seminar, Department of Mathematics, , University of California, Berkeley, Oct 29, 2008.
  28. Are we ready for OMICS of recombinations? Data Mining for Biomedical Applications , University of Florida, Gainesville, Florida, Oct 1, 2008.
  29. Mathematics of Motifs in Biology, Lecture Series on [Re]Sequencing and Annotation of Genomes, International School on Biology, Computation and Information (BCI), Cluster in Biomedicine (CBM), Bassovizza, Trieste, Italy, Sept 08-12, 2008.
  30. Exploring the Recombinant Genome for Phylogeography, Universita Delgi Studi di Padova, Padua, Italy, Sept 04, 2008.
  31. Taming Patterns in Biological Data, Keynote address at Data Mining for Biomedical Informatics, 8th SIAM International Conference on Data Mining (SDM 2008), Atlanta, April 24-26, 2008.
  32. Algorithms For Inferring Deep Ancestry, Innovation in Drug Discovery and Development, IBM Life Sciences Virtual Expo, April 16-17, 2008.
  33. Taming Patterns through Combinatorics in Bioinformatics, Parc de Recerca Biomedica de Barcelona (PRBB), Barcelona, March 26, 2008.
  34. Combinatorics and Statistics of Gene Clusters, ACO (Algorithms, Combinatorics and Optimizations) Seminar, School of Mathematics, Georgia Tech, Atlanta, Feb 29, 2008.
  35. Combinatorics and Statistics of Gene Clusters, Mathematics of Knowledge and Search Engines: Search and Knowledge Building for Biological Datasets, IPAM (Institute for Applied and Pure Mathematics), University of California, Los Angeles, Nov 26-30, 2007.
  36. Combinatorics and Statistics of Gene Clusters, IBM Watson Research Math Seminar Series, Nov 9, 2007.
  37. Theory and Algorithms of Patterns, tutorial at the ISMB & ECCB (Intelligent Systems for Molecular Biology & European Conference on Computational Biology), Vienna, Austria, July 21-25, 2007.
  38. Combinatorics in Bioinformatics: Permutations and Applications, Genome Biology and Bioinformatics (GBB) Retreat, University of Toronto, Toronto, May 31, 2007.
  39. Pattern Discovery in Bioinformatics, IMA/MCIM Industrial problems seminar, Institute for Mathematics and its Applications/Minnesota Center for Industrial Math, University of Minnesota, Minneapolis, May 4, 2007.
  40. Permutations in Bioinformatics, Department of Computer Science, New Jersey Institute of Technology, Newark, April 30, 2007.
  41. Some Applications of Combinatorics in Bioinformatics, Physics Seminar, The Institute of Mathematical Sciences, Chennai, Dec 29, 2006.
  42. What can Bioinformatics do for you?, Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore, Dec 28, 2006.
  43. Permutations in Bioinformatics, Computational Insights into Biological Systems, Indian Institute of Sciences, Bangalore, Dec 26-28, 2006.
  44. Permutations in Bioinformatics, International Conference on Bioinformatics, InCoB, Delhi, December 18-20, 2006.
  45. Generalized Permutation Patterns: Theory, Algorithms & Applications, at Center for Computational Biology and Bioinformatics, Columbia University Medical Center, June 08, 2006.
  46. Topological Motif Discovery, jointly with David Gilbert, Bioinformatics Research Center, University of Glasgow, at Schloss Dagstuhl, Internationales Begegnungs und Forschungszentrum fur Informatik, Germany. May 17, 2006.
  47. Gapped Permutation Patterns with Bounded Length, Schloss Dagstuhl, Internationales Begegnungs und Forschungszentrum fur Informatik, Germany. May 15, 2006.
  48. A Common Framework for Mining Motifs in Diverse Data, Department of Computer Science, New Jersey Institute of Technology, Newark, April 18, 2005.
  49. Topological motifs: can stringology help? The Second Haifa Annual International Stringology Research Workshop of the Israel Science Foundation, The Caesarea Edmond Benjamin de Rothschild Foundation, Institute for Interdisciplinary Applications of Computer Science, Haifa, April 3-8, 2005. (conference photos by Stefano, by Laurant, by Veli)
  50. Combinatorics and Statistics of Motifs, IBM Haifa Research Lab, Haifa, Israel, April 4, 2005.
  51. Exploiting Patterns in Biological Data, Computer Science Distinguished Lecture Series, Arizona State University, Tempe, March 28, 2005.
  52. A Uniform Framework for Studying Patterns in Data, National University of Singapore, Singapore, Jan 20, 2005.
  53. Unusual Motifs in Biological Data, Computer Science & Engineering Colloquia Series, Michigan State University, East Lansing, Nov 15, 2004.
  54. Discovering Patterns for Understanding Biological Data, New York Academy of Sciences, Nov 10, 2004.
  55. Exploiting Regularities in Biological Data, Computer Science Colloquium, City University of New York, October 7, 2004.
  56. Unusual Motifs in Biological Data, Department of Computer Science Colloquia Series, and seminar series in Bioinformatics Research Center, North Carolina State University, Raleigh, Sept 30, 2004.
  57. Permutation and Other Motifs, School of Computer Science, Tata Institute of Fundamental Research, Mumbai, Sept 3, 2004.
  58. Towards Understanding Large Volume Biological Data, tutorial at Utkal University, Bhubaneswar, August 30, 2004.
  59. A formal treatment of the problem of Pattern Discovery, tutorial at the ISMB & ECCB (Intelligent Systems for Molecular Biology & European Conference on Computational Biology), Glasgow, UK, July 31-Aug 4, 2004.
  60. Understanding Biological Data Through Patterns, Seminar series, Othmer Institute for Interdisciplinary Studies, Polytechnic University, New York, May 19, 2004.
  61. On the Problem of Extensible Substring Patterns, General Theory of Information Transfer and Combinatorics, Zentrum fur interdisziplinare Forschung, Bielefeld, Germany, April 26-30, 2004.
  62. Permutation Motifs in Biological Data, Bioinformatics Symposium, The Center for Advanced Computer Studies, University of Louisiana, Lafayette, April 8, 2004.
  63. Permutation Patterns, Departement d'Informatique et de Recherche Operationnelle, (Laboratoire de Biologie informatique et Theorique), Unversite de Montreal, Montreal, Feb 5-6, 2004.
  64. Exploiting Regularities in Data for Bioinformatics, Computer Science and Information Technology, RMIT University, Melbourne, Australia, July 4, 2003.
  65. Flexible Pattern Discovery based on Inexact-Suffix Trees, Zentrum fur interdisziplinare Forschung, Bielefeld, Germany, February 18-20, 2003.
  66. Permutation Patterns and Bioinformatics, General Theory of Information Transfer and Combinatorics, Zentrum fur interdisziplinare Forschung, Universitat Bielefeld, Bielefeld, Germany, November 3-9, 2002. (at Bielefeld palace with the Mayor)
  67. Bioinformatics and Pattern Discovery , University of Maryland, College Park, April 29, 2002.
  68. Bioinformatics and Pattern Discovery , Yale University, New Haven, April 9, 2002.
  69. Bioinformatics and Pattern Discovery , Johns Hopkins University, Baltimore, March 15, 2002.
  70. Computational Biology and Pattern Discovery , Theory Day 2001, New York, November 16, 2001.
  71. Discovering Information from Data , WORDS 2001, Palermo, September 17-21, 2001.
  72. The Role of Algorithms in Bioinformatics, Biofuture 2001, Toronto, September 5-7, 2001.
  73. Pattern Discovery and Applications, Sequence Analysis and Annotation, Symposium on Computational Genetics , Cleveland, October 20, 2000.
  74. Flexible Pattern Discovery , Summer School at the Eleventh Annual Symposium on Combinatorial Pattern Matching, Montreal, June 19-20, 2000.
  75. Motif Discovery in Computational Biology, Computational Biology and Bioinformatics Lecture Series, Department of Electrical Engineering and Computer Science, Case Western Reserve University, Cleveland, December 13, 1999.
  76. Pattern Discovery in Sequence Data: Linear Bound on a Basis Set, Computer and Information Science Seminar Series, Brooklyn Polytechnic University, New York, November 29, 1999.
  77. Pattern Discovery: Theory and Practice, Workshop on Knowledge Management: Moving from Business to Technical and Scientific Domains, CASCON, Toronto, Canada, November 9, 1999.
  78. Mulitple Sequence Alignment using MUSCA , Columbia Genome Center, Columbia University , New York, October 15, 1999.
  79. Motif Discovery and Applications, Computer Science Colloquium, Graduate School and University Center, City University of New York, May 25, 1999.
  80. An Algorithm for Multiple Sequence Alignment, IBM India Research Laboratory, New Delhi, April 23, 1999.
  81. Theoretical Issues in Single Molecule Methods, Department of Computer Science, University of Auckland, Auckland, January 14, 1999.
  82. Problem of Physical Mapping in Single Molecule Methods, Department of Information Science, University of Tokyo, Tokyo, December 11, 1998.
  83. Algorithmic Issues in Computational Genomics, IBM Thomas J Watson Research Center, March 19, 1998.
  84. Algorithmic Issues in Computational Genomics, Department of Computer Science, University of Georgia, Athens, March 17, 1998.
  85. Algorithmic Issues in Computational Genomics, Department of Mathematical and Computer Sciences, Loyola University Chicago, Chicago, March 13, 1998.
  86. Algorithmic Issues in Computational Genomics, Department of Computer Science, University of Iowa, Iowa City, March 9, 1998.
  87. Algorithmic Issues in Computational Genomics, Department of Computer Science, State University of New York Stony Brook, March 4, 1998.
  88. Algorithms for Single Molecule Methods , Department of Computer Science, SUNY Brockport, Brockport, February 23, 1998.

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