Laxmi Parida  Laxmi Parida photo       

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Distinguished RSM & Manager, Computational Genomics Group
Thomas J. Watson Research Center, Yorktown Heights, NY USA
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Professional Associations

Professional Associations:  ACM  |  International Society for Computational Biology  |  Society for Industrial and Applied Mathematics

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More information:  Group page


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

    Book

  • Pattern Discovery in Bioinformatics: Theory and Algorithms.
    Author: Laxmi Parida
    Publisher: Chapman & Hall/CRC; 1 edition (July 16, 2007), 532 pages,
    ISBN-10: 1584885491, ISBN-13: 978-1584885498.
    table of contents & reviews (CS Top-4 list)

  • Edited Volumes

  • Proceedings of Eighth Asia-Pacific Bioinformatics Conference (APBC 2010)
    Editors: Laxmi Parida and Gene Myers
    BMC Bioinformatics 2010, 11(Suppl 1):I1 (18 January 2010)

  • Combinatorial Pattern Matching,
    Editors: Amihood Amir and Laxmi Parida
    LNCS 6129 Springer-Verlag 2010, ISSN 0302-9743, 2010.

  • Information and Computation,
    Editors: Amihood Amir and Laxmi Parida
    Elsevier, 2011.

    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. Genetic History of Populations: Limits to Inference,
    Authors: Daniel E Platt, Filippo Utro, Marc Pybus and Laxmi Parida
    Models and Algorithms for Genome Evolution
    Editor: Cedric Chauve, Nadia El-Mabrouk and Eric Tannier
    2013.
    Publisher: Springer.

  5. Modeling/Algorithmics

  6. Exploring differentially expressed genes and pathways under drought, flooding and salinity conditions in reed canary grass (Phalaris arundinacea), an autopolyploid C3 forage and bioenergy grass species, Manfred Klaas, Niina Haiminen, Filippo Utro, Tia Vellani, Cora Muennich, Thomas Didion, Christian Sig Jensen, Laxmi Parida, Susanne Barth, Plant Biology Europe (FESPB) Dublin, Ireland, June22-26, 2014.
  7. Effect of sampling on the extent and accuracy of the inferred genetic history of recombining genome, Daniel E Platt, Filippo Utro, and Laxmi Parida, Computational Biology and Chemistry, APBC 2014.
  8. Spectral sequences, exact couples and persistent homology of filtrations, Saugata Basu, Laxmi Parida 2013. archived
  9. BAC Sequencing Using Pooled Methods, Saski CA, Feltus FA, Parida L, Haiminen N, submitted 2013.
  10. Limitations to determining genetic history in the recombinant genome and connection to demographic events from samples of modern populations (abstract) Daniel E Platt, Filippo Utro, and Laxmi Parida, ASHG 2013.
  11. MINT: Mutual Information based Transductive Feature Selection for Genetic Trait Prediction, Dan He,Irina Rish, David Haws, Simon Teyssedre, Zivan Karaman, Laxmi Parida, The Seventh International Workshop on Machine Learning in Systems Biology (MLSB 2013), Berlin, Germany, July 21 - 23, 2013.
  12. Using Random Graphs in Population Genomics (abstract). L. Parida, The Nature of Computation. Logic, Algorithms, Applications (Lecture Notes in Computer Science), Springer Verlag, 2013.
  13. iXora: Exact haplotype inferencing and trait association BMC Genetics 2013, 14:48 doi:10.1186/1471-2156-14-48
  14. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color, Genome Biology 2013, 14:R53 doi:10.1186/gb-2013-14-6-r53. Editor's pick.
  15. Irredundant Tandem Motifs, Laxmi Parida, Cinzia Pizzi, and Simona E. Rombo, Theoretical Computer Science 2013.
  16. Efficient in-silico chromosomal representation of populations via indexing ancestral genomes, Niina Haiminen, Filippo Utro, Claude Lebreton, Pascal Flament, Zivan Karaman and Laxmi Parida, Algorithms, 2013, 6, 430-441.
  17. Transductive HSIC Lasso, Dan He, Irina Rish and Laxmi Parida, submitted, 2013.
  18. Ultrametric networks: a new tool for phylogenetic analysis, Apostolico Alberto, Comin Matteo, Dress Andreas, Parida Laxmi, Algorithms for Molecular Biology.2013, 8:7. DOI: 10.1186/1748-7188-8-7
  19. IPED: Inheritance Path based Pedigree Reconstruction Algorithm using Genotype Data, Dan He, Zhanyong Wang, Laxmi Parida and Eleazar Eskin, RECOMB 2013.
  20. Sum of parts is greater than the whole: inference of common genetic history of populations, Filippo Utro, Marc Pybus, and Laxmi Parida, APBC 2013, BMC Genomics 2013, 14(Suppl 1):S10 doi:10.1186/1471-2164-14-S1-S10. .
  21. ARG-based Genome-wide Analysis of Cacao Cultivars, Filippo Utro, Omar E. Cornejo, Don Livingstone, Juan Carlos Motamayor, and Laxmi Parida, RECOMB-CG 2012, BMC Bioinformatics.
  22. Ganeshprasad Arunkumar, David F Soria-Hernanz, Valampuri John Kavitha, Varatharajan Santhakumari Arun, Adhikarla Syama, Kumaran Samy Ashokan, Kavandanpatti Thangaraj Gandhirajan, Koothapuli Vijayakumar, Muthuswamy Narayanan, Mariakuttikan Jayalakshmi, Janet S Ziegle, Ajay K Royarru, Laxmi Parida, R Spencer Wells, Colin Renfrew, Theodore G. Schurr, Chris Tyler Smith, Daniel E Platt, Ramasamy Pitchappan and The Genographic Consortium (2012),"Population differentiation of Southern Indian Male Lineages Correlates with Agricultural Expansions Predating the Caste System," PLoS One.
  23. Characterization and Extraction of Irredundant Tandem Motifs, Laxmi Parida, Cinzia Pizzi, and Simona E. Rombo, SPIRE 2012.
  24. Javed, A., Pybus, M., Mel, 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.
  25. Recombination networks as genetic markers: a human variation study of the Old World, Javed, A., Mel, 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
  26. The footprint of recombination gives a new insight in the effective population size and the history of the Old World human populations, Mel, 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
  27. 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, Annual Symposium of AMIA (American Medical Informatics Association), Oct 22-26, Washington, DC, 2011.
  28. 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.
  29. 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
  30. Assessing Pooled BAC and Whole Genome Shotgun Strategies for Complex Genome Assembly, Niina Haiminen, F. Alex Feltus, Laxmi Parida, BMC Genomics, 2011.
  31. 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.
  32. 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.
  33. Recombinomics: Population Genomics from a Recombination Perspective, Asif Javed, Laxmi Parida, Proceedings of C3S2E, Montreal, 2010.
  34. Combinatorics in Recombinational Population Genomics, Laxmi Parida, ISBRA 2010, LNBI 6053, pp. 126--127, 2010 (Keynote Abstract).
  35. Ancestral Recombinations Graph: A Reconstructability Perspective using Random-Graphs Framework, Laxmi Parida, Journal of Computational Biology, 2010.
  36. 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.
  37. Minimizing Recombinations in Consensus Networks for Phylogeographic Studies, Laxmi Parida, Asif Javed, Marta Mele, Francesc Calafell, Jaume Bertranpetit, BMC Bioinformatics , APBC, Beijing, 2009.
  38. A case for Recombinomics, Laxmi Parida, Asif Javed, Marta Mele, Jaume Bertranpetit, IBM Technical Report RC24677, August, 2008.
  39. 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.
  40. Detection of Subtle Variations as Consensus Motifs, Matteo Comin, Laxmi Parida, Theoretical Computer Science, 395(2-3), pp 158-170, May, 2008.
  41. 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.
  42. Statistical Significance of Large Gene Clusters, Laxmi Parida, Journal of Computational Biology, 14(9), pp 1145--1159, 2007.
  43. Gapped Permutation Pattern Discovery for Gene Order Comparisons, Laxmi Parida, Journal of Computational Biology, vol 14, No 1, pp 46-56, 2007.
  44. Using PQ Structures for Genomic Rearrangement Phylogeny, Laxmi Parida, Journal of Computational Biology, 13(10), pp 1685-1700, 2006
  45. 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.
  46. 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.
  47. Motif Patterns in 2D, Alberto Apostolico, Laxmi Parida, Simona E. Rombo, Theoretical Computer Science, vol 390, N0 1, pp 40-55, 22 January 2008.
  48. 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.
  49. Constructing Near-Perfect Phylogenies with Multiple Homoplasy Events R V Satya, A Mukherji, G Alexe, L Parida, G Bhanot, ISMB, Bioinformatics, 514-522, 2006.
  50. Using Permutation Patterns for Content-Based Phylogeny, Enam Karim, Laxmi Parida, Arun Lakhotia, Pattern Recognition in Bioinformatics, LNBI 4146, pp 115-125, 2006.
  51. Modeling the Combinatorial Control of Transcription using Partial Order Motifs and their Redescriptions, Naren Ramakrishnan and Laxmi Parida, under submission 2006.
  52. Gapped Permutation Patterns for Comparative Genomics, Laxmi Parida, Proceedings of WABI, Algorithms in Bioinformatics, LNBI 4175, pp 376-387, 2006.
  53. A PQ Framework for Reconstructions of Common Ancestors & Phylogeny Laxmi Parida, Proceedings of RECOMB-CG, Comparative Genomics, LNBI 4205, pp 141-155, 2006.
  54. 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.
  55. Discovering Topological Motifs Using a Compact Notation, Laxmi Parida, Journal of Computational Biology, 14(3), pp 46--69, 2007.
  56. 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.
  57. Mining, Compressing and Classifying with Extensible Motifs, A. Apostolico, M. Comin, L. Parida, , 2005.
  58. 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.
  59. Malware Phylogeny Generation Using Permutations of Code, M E Karim, A Walenstein, A Lakhotia, L Parida, Journal in Computer Virology, 2005.
  60. Redescriptions: Strucutre Theory & Algorithms, Laxmi Parida, Naren Ramakrishnan, AAAI 2005, Pittsburgh, pp 837-844, July 9-13, 2005.
  61. 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.
  62. Malware Phylogeny Using Maximal pi-Patterns, Arun Lakhotia, Md Enamul Karim, Andrew Walenstein, Laxmi Parida, EICAR 2005, Malta, April 30-May 3, 2005.
  63. Off-line Compression by Extensible Motifs, A. Apostolico, M. Comin, L. Parida, Data Compression Conference (DCC), Snowbird, Utah, March 29-31, 2005.
  64. Conservative Extraction of Over-represented Motifs, A. Apostolico, M. Comin, L. Parida, ISMB 2005 Michigan, pp 9-18, June 25-29, 2005. abstract, PDF.
  65. 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.
  66. 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.
  67. Permutation Pattern Discovery in Biosequences, R Eres, G M Landau, L Parida, Journal of Computational Biology, vol 11, No 6, pp 1050-1060, 2004.
  68. Incremental Paradigms of Motif Discovery, Alberto Apostolico, Laxmi Parida, Journal of Computational Biology, vol 11, No 1, pp 15-25, 2004.
  69. An inexact suffix tree based algorithm for extensible pattern discovery, Abhijit Chattaraj, Laxmi Parida, Theoretical Computer Science, 335:1, pp 3-14, 2005.
  70. 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.
  71. 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)
  72. 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.
  73. Developing a similarity measure in biological function space, Ronald Jensen, Haiyuan Yu, Laxmi Parida, Gustavo Stolovitzky, Mark Gerstein, 2003.
  74. 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.
  75. Dictionary-driven Protein Annotation, Isidore Rigoutsos, Tien Huynh, Aris Floratos, Laxmi Parida, Daniel Platt, Nucleic Acid Research, 2002, Vol 30 No 17 3901--3916.
  76. TeiresiasP: Parallelized Data Mining for Shared and Distributed Environments, Tien Huynh, Laxmi Parida, Daniel Platt, Isidore Rigoutsos, under submission, 2002.
  77. 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.
  78. 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 )
  79. 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.
  80. 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.
  81. Some Results on Flexible-pattern Discovery, Laxmi Parida, Combinatorial Pattern Matching (CPM 2000), LNCS vol 1848, pp 33--45, 2000.
  82. 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.
  83. 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.
  84. 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.
  85. 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)
  86. 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.
  87. 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.
  88. 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.
  89. Population genomics

    (as Genographic Consortium)
  90. 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).
  91. 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).
  92. 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).
  93. 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).
  94. 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).
  95. 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, Lpez-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).
  96. 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).
  97. 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).
  98. 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).
  99. 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).
  100. 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).
  101. Single Molecule Methods

  102. 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.
  103. 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.
  104. Algorithmic Complexity of Physical Mapping Problems Arising in Single Molecule Methods, Laxmi Parida, IBM Technical Report, 1998.
  105. 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.
  106. 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.
  107. 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.
  108. 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.
  109. A Model and Solution to the DNA Flipping String Problem, Davi Geiger, Laxmi Parida, Courant Inst. of Math. Sciences, NYU, TR1996-720, May 1996.
  110. 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.
  111. 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.
  112. Thesis

  113. 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.)

  114. Computer Vision

  115. 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 .
  116. 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.
  117. 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.
  118. 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.
  119. Geometric Computing

  120. 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.
  121. Computational Methods for Evaluating Swept Object Boundaries, Laxmi Parida, S.P. Mudur, 10:266-276, The Visual Computer, 1994.
  122. 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 .)
  123. 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 .)
  124. A Computational Technique for General Shape Deformations for use in Font Design, Laxmi Parida, Vol 17, No. 4, Computers & Graphics, pp. 349-356, 1993.
  125. 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 .)
  126. Social Software

  127. 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.
  128. 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.