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Research Publications

Please contact me or use to get copies of the papers below

    Book Chapters

  1. BAC Sequencing Using Pooled Methods,
    Author: Christopher A. Saski, F. Alex Feltus, Laxmi Parida, Niina Haiminen
    Bacterial Artificial Chromosomes, Methods in Molecular Biology Volume 1227, 2015, pp 55-67.
    Publisher: Springer Verlag, 2015.

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

  3. 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.

  4. 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.

  5. 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.

  6. Modeling/Algorithmics

  7. Glioblastoma treatment identification: comparing strategies for sequencing and curation, under submission 2017.
  8. A quantitative and qualitative characterization of the k-mer analysis of short sequences, Daniel Platt, Filippo Utro, Laxmi Parida, CIBB, 2017.
  9. Host phenotype prediction from differentially abundant microbes using RoDEO, Anna Paola Carrieri, Niina Haiminen and Laxmi Parida, LNBI, 2017.
  10. Application of genome wide association and genomic prediction for improvement of cacao against black and frosty pod diseases, J. Alberto Romero Navarro, Wilbert Wilbert Phillips-Mora, Adriana Arciniegas-Leal, Allan Mata-Quirós, Niina Haiminen, Guiliana Mustiga, Donald Livingstone III, Harm Van bakel, David Kuhn, Laxmi Parida, Andrew Kasarskis, Juan Carlos Motamayor, Frontiers in Plant Science, 2017.
  11. Comparing sequencing assays and human-machine analyses in actionable genomics for glioblastoma, Kazimierz O. Wrzeszczynski, Mayu O. Frank, Takahiko Koyama, Kahn Rhrissorrakrai, Nicolas Robine, Filippo Utro, Anne-Katrine Emde, Bo-Juen Chen, Kanika Arora, Minita Shah, Vladimir Vacic, Raquel Norel, Erhan Bilal, Ewa A. Bergmann, Julia Moore-Vogel, Jeffrey Bruce, Andrew Lassman, Peter Canoll, Christian Grommes, Steve Harvey, Laxmi Parida, Vanessa V. Michelini, Michael C. Zody, Vaidehi Jobanputra, Ajay K. Royyuru, and Robert B. Darnell. Neurology: Genetics, July, 2017.
  12. Enhancing NGS-Guided Cancer Care Through Cognitive Computing, The Oncologist, 2017.
  13. Genetic variation reveals sociolinguistic stratification within Indian subcontinent and highlights on its demographic history, Aritra Bose , Daniel Platt , Laxmi parida , Peristera Paschou, Petros Drineas, under submission, 2017.
  14. Characterizing differentially expressed genes under flooding and drought stress in the grasses Phalaris arundinacea and Dactylis glomerata, Manfred Klaas, Niina S Haiminen, Jim Grant, Paul Cormican, John Finnan, Sai Arojju Krishna, Filippo Utro, Tia Vellani, Laxmi Parida, and Susanne Barth, under submission, 2017.
  15. IPED2: Inheritance Path based Pedigree Reconstruction Algorithm for Complicated Pedigrees, Dan He, Zhanyong Wang, Laxmi Parida, Eleazar Eskin, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol PP: 99, 28 March, 2017.
  16. MUSE: A Multi-locus Sampling-based Epistasis Algorithm for Quantitative Genetic Trait Prediction, Dan He, Laxmi Parida, Pacific Symposium on Biocomputing Hawaii, Jan 3-7 2017.
  17. Design of the MCAW compute service for food safety bioinformatics, IBM Journal of Research and Development, Vol 60:5/6, Sept.-Nov. 2016. Page(s):2:1-2:12, DOI:10.1147/JRD.2016.2584798.
  18. Efficient Algorithms for Sequence Analysis with Entropic Profiles, Cinzia Pizzi, Mattia Ornamenti, Simone Spangaro, Simona E. Rombo and Laxmi Parida, to appear in TCBB 2016.
  19. Genetic Variation reveals migrations into the Indian subcontinent and its influence on the Indian society. (abstract) Aritra Bose, Daniel E. Platt, Laxmi Parida, Peristera Paschou, Petros Drineas, ASHG 2016.
  20. Testing differential genetic flow across Sinai and Bab-el-Mandeb. (abstract) Daniel E. Platt, Laxmi Parida, Saugata Basu, Pierre Zalloua, ASHG 2016.
  21. Understanding False Positives in Mapping of Microbiome Sequence Data Using In-silico Simulations, abstract at International Association for Food Protection IAFP 2016.
  22. Scalable Algorithms at Genomic Resolution to fit LD Distributions, Laxmi Parida and Niina Haiminen, ACM-BCB 2016.
  23. Dimension reduction of metagenome data using RoDEO improves phenotype prediction, Anna Paola Carrieri, Niina Haiminen and Laxmi Parida, Computational Intelligence methods for Bioinformatics and Biostatistics, CIBB 2016.
  24. Watson for Genomics: Moving Personalized Medicine Forward, Kahn Rhrissorrakrai, Takahiko Koyama, Laxmi Parida, Trends in Cancer, 2016.
    (Watson for Genomics) Precision medicine/ clinical oncology Abstracts:
    Keystone Feb 2016: Watson Genomic Analytics: Literature-informed Dynamic Computational Model for Molecularly Targeted Therapies.
    ASHG Nov 2015: Case analysis of advanced cancers with Watson Genomic Analytics.
  25. Novel Applications of Multi-task Learning and Multiple Output Regression to Multiple Genetic Trait Prediction, Dan He, David Kuhn, Laxmi Parida, Bioinformatics, vol 32, issue 12, pp 37-43, ISMB Orlando, June 2016.
  26. Spectral sequences, exact couples and persistent homology of filtrations, Saugata Basu, Laxmi Parida, Expositiones Mathematicae 2016.
  27. Accurate and efficient sampling of underlying ARG of multiple populations under subdivision and admixture, Anna Paola Carrieri, Filippo Utro, Laxmi Parida, Bioinformatics, 2015. doi: 10.1093/bioinformatics/btv716
  28. Characterizing redescriptions using persistent homology to isolate genetic pathways contributing to pathogenesis, Daniel Platt, Saugata Basu, Pierre Zalloua and Laxmi Parida, APBC, San Francisco, BMC Systems Biology, 2016.
  29. Variable-Selection Emerges on Top in Empirical Comparison in Whole Genome Trait Prediction, David Haws, Irina Rish, Simon Tesseydre, Dan He, Aurelie Lozano, Prabhanjan Kambadur, Zivan Karaman, Laxmi Parida, PLOS ONE,, 2015.
  30. Does Encoding Matter? A Novel View On The Quantitative Genetic Trait Prediction Problem, Dan He, Laxmi Parida, IEEE International Conference on Bioinformatics and Biomedicine (IEEE BIBM), Washington DC, 2015.
  31. Performance evaluation of different encoding strategies for quantitative Genetic trait prediction, Dan He, Oyetunji E. Ogundijo, Laxmi Parida, 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences (IEEE ICCABS), Miami, 2015.
  32. SAME: A sampling-based multi-locus epistasis algorithm for quantitative genetic trait prediction, Dan He, Laxmi Parida, The ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), Atlanta, 2015.
  33. Reducing false-negative exclusion of GWAS by using redescription and computational topological analysis to identify complex phenotypes describing pathways. (abstract) Daniel E. Platt, Pierre Zalloua, Saugata Basu, and Laxmi Parida, ASHG 2015.
  34. SimBA: Simulation Algorithm to Fit Extant-Population Distributions, Laxmi Parida, Niina Haiminen, BMC Bioinformatics, 2015.
  35. Topological Signatures for Population Admixture, Laxmi Parida, Filippo Utro, Deniz Yorukoglu, David Kuhn, Saugata Basu, RECOMB, Warsaw, LNBI 9029, pp 261-275, 2015
  36. Host Trait Prediction of Metagenomic Data for Topology-based Visualization, Laxmi Parida, Niina Haiminen, David Haws, Jan Suchodski, ICDCIT, LNCS 8956, pp 134-149, 2015
  37. Data-driven Encoding for Genetic Trait Prediction, Dan He, Zhanyong Wang, Laxmi Parida, BMC Bioinformatics, 16(Suppl 1):S10; DOI: 10.1186/1471-2105-16-S1-S10 2015
    Presented at APBC, HsinChu, Taiwan, 2015.
  38. Comparative exomics of Phalaris cultivars under salt stress, Niina Haiminen, Manfred Klaas, Zeyu Zhou, Filippo Utro, Paul Cormican, Thomas Didion, Christian Sig Jensen, Christopher E Mason, Susanne Barth and Laxmi Parida, BMC Genomics 2014, 15(Suppl 6):S18
  39. SimRA: Rapid and Accurate Simulation of Populations based on Random-Graph Models of ARG, Anna Paola Carrieri, Laxmi Parida, Recomb-CG 2014 (poster).
  40. K-mer Analysis of Ebola sequences differentiates outbreaks, Filippo Utro, Daniel E. Platt and Laxmi Parida, Recomb-CG 2014 (poster).
  41. Topological Data Analysis to detect population admixture in recombining chromosomes, Filippo Utro, Deniz Yorukoglu, David Kuhn, Saugata Basu and Laxmi Parida, Recomb-CG 2014 (poster).
  42. Beta and Gamma human papillomaviruses have different evolutionary histories, Zigui Chen, Filippo Utro, Daniel Platt, Laxmi Parida, Robert Desalle and Robert D Burk, under review, 2014.
  43. Entropic profiles, maximal motifs and the discovery of significant repetitions in genomic sequences, Laxmi Parida, Cinzia Pizzi and Simona E. Rombo, Algorithms in Bioinformatics, Lecture Notes in Computer Science Volume 8701, 2014, pp 148-160. WABI, Wroclaw, Poland, September 8-10, 2014.
  44. Best-Fit in Linear Time for Non-generative Population Simulation, Niina Haiminen, Claude Lebreton, Laxmi Parida, Algorithms in Bioinformatics, Lecture Notes in Computer Science Volume 8701, 2014, pp 247-262. WABI, Wroclaw, Poland, September 8-10, 2014.
  45. 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, June 22-26, 2014.
  46. 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.
  47. 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.
  48. 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.
  49. Using Random Graphs in Population Genomics (abstract). L. Parida, The Nature of Computation. Logic, Algorithms, Applications (Lecture Notes in Computer Science), Springer Verlag, 2013.
  50. iXora: Exact haplotype inferencing and trait association BMC Genetics 2013, 14:48 doi:10.1186/1471-2156-14-48
  51. 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.
  52. Irredundant Tandem Motifs, Laxmi Parida, Cinzia Pizzi, and Simona E. Rombo, Theoretical Computer Science, vol 525, pp 89-102, 2013.
  53. 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.
  54. 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
  55. IPED: Inheritance Path based Pedigree Reconstruction Algorithm using Genotype Data, Dan He, Zhanyong Wang, Laxmi Parida and Eleazar Eskin, RECOMB 2013.
  56. 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.
  57. 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.
  58. 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.
  59. Characterization and Extraction of Irredundant Tandem Motifs, Laxmi Parida, Cinzia Pizzi, and Simona E. Rombo, SPIRE 2012.
  60. 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.
  61. 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
  62. 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
  63. 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.
  64. 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.
  65. 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
  66. Assessing Pooled BAC and Whole Genome Shotgun Strategies for Complex Genome Assembly, Niina Haiminen, F. Alex Feltus, Laxmi Parida, BMC Genomics, 2011.
  67. 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.
  68. 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.
  69. Recombinomics: Population Genomics from a Recombination Perspective, Asif Javed, Laxmi Parida, Proceedings of C3S2E, Montreal, 2010.
  70. Combinatorics in Recombinational Population Genomics, Laxmi Parida, ISBRA 2010, LNBI 6053, pp. 126--127, 2010 (Keynote Abstract).
  71. Ancestral Recombinations Graph: A Reconstructability Perspective using Random-Graphs Framework, Laxmi Parida, Journal of Computational Biology, 2010.
  72. 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.
  73. Minimizing Recombinations in Consensus Networks for Phylogeographic Studies, Laxmi Parida, Asif Javed, Marta Mele, Francesc Calafell, Jaume Bertranpetit, BMC Bioinformatics , APBC, Beijing, 2009.
  74. A case for Recombinomics, Laxmi Parida, Asif Javed, Marta Mele, Jaume Bertranpetit, IBM Technical Report RC24677, August, 2008.
  75. 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.
  76. Detection of Subtle Variations as Consensus Motifs, Matteo Comin, Laxmi Parida, Theoretical Computer Science, 395(2-3), pp 158-170, May, 2008.
  77. 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.
  78. Statistical Significance of Large Gene Clusters, Laxmi Parida, Journal of Computational Biology, 14(9), pp 1145--1159, 2007.
  79. Gapped Permutation Pattern Discovery for Gene Order Comparisons, Laxmi Parida, Journal of Computational Biology, vol 14, No 1, pp 46-56, 2007.
  80. Using PQ Structures for Genomic Rearrangement Phylogeny, Laxmi Parida, Journal of Computational Biology, 13(10), pp 1685-1700, 2006
  81. 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.
  82. 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.
  83. Motif Patterns in 2D, Alberto Apostolico, Laxmi Parida, Simona E. Rombo, Theoretical Computer Science, vol 390, N0 1, pp 40-55, 22 January 2008.
  84. 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.
  85. Constructing Near-Perfect Phylogenies with Multiple Homoplasy Events R V Satya, A Mukherji, G Alexe, L Parida, G Bhanot, ISMB, Bioinformatics, 514-522, 2006.
  86. Using Permutation Patterns for Content-Based Phylogeny, Enam Karim, Laxmi Parida, Arun Lakhotia, Pattern Recognition in Bioinformatics, LNBI 4146, pp 115-125, 2006.
  87. Gapped Permutation Patterns for Comparative Genomics, Laxmi Parida, Proceedings of WABI, Algorithms in Bioinformatics, LNBI 4175, pp 376-387, 2006.
  88. A PQ Framework for Reconstructions of Common Ancestors & Phylogeny Laxmi Parida, Proceedings of RECOMB-CG, Comparative Genomics, LNBI 4205, pp 141-155, 2006.
  89. 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.
  90. Discovering Topological Motifs Using a Compact Notation, Laxmi Parida, Journal of Computational Biology, 14(3), pp 46--69, 2007.
  91. 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.
  92. Mining, Compressing and Classifying with Extensible Motifs, A. Apostolico, M. Comin, L. Parida, , 2005.
  93. 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.
  94. Malware Phylogeny Generation Using Permutations of Code, M E Karim, A Walenstein, A Lakhotia, L Parida, Journal in Computer Virology, 2005.
  95. Redescriptions: Strucutre Theory & Algorithms, Laxmi Parida, Naren Ramakrishnan, AAAI 2005, Pittsburgh, pp 837-844, July 9-13, 2005.
  96. 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.
  97. Malware Phylogeny Using Maximal pi-Patterns, Arun Lakhotia, Md Enamul Karim, Andrew Walenstein, Laxmi Parida, EICAR 2005, Malta, April 30-May 3, 2005.
  98. Off-line Compression by Extensible Motifs, A. Apostolico, M. Comin, L. Parida, Data Compression Conference (DCC), Snowbird, Utah, March 29-31, 2005.
  99. Conservative Extraction of Over-represented Motifs, A. Apostolico, M. Comin, L. Parida, ISMB 2005 Michigan, pp 9-18, June 25-29, 2005. abstract, PDF.
  100. 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.
  101. 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.
  102. Permutation Pattern Discovery in Biosequences, R Eres, G M Landau, L Parida, Journal of Computational Biology, vol 11, No 6, pp 1050-1060, 2004.
  103. Incremental Paradigms of Motif Discovery, Alberto Apostolico, Laxmi Parida, Journal of Computational Biology, vol 11, No 1, pp 15-25, 2004.
  104. An inexact suffix tree based algorithm for extensible pattern discovery, Abhijit Chattaraj, Laxmi Parida, Theoretical Computer Science, 335:1, pp 3-14, 2005.
  105. 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.
  106. 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)
  107. 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.
  108. 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.
  109. Dictionary-driven Protein Annotation, Isidore Rigoutsos, Tien Huynh, Aris Floratos, Laxmi Parida, Daniel Platt, Nucleic Acid Research, 2002, Vol 30 No 17 3901--3916.
  110. 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.
  111. 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 )
  112. 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.
  113. 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.
  114. Some Results on Flexible-pattern Discovery, Laxmi Parida, Combinatorial Pattern Matching (CPM 2000), LNCS vol 1848, pp 33--45, 2000.
  115. 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.
  116. 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.
  117. 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.
  118. 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)
  119. 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.
  120. 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.
  121. 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.
  122. Population genomics

    (as Genographic Consortium)
  123. Aboriginal Australian mitochondrial genome variation ? an increased understanding of population antiquity and diversity, Nagle etal, Sci Rep. 2017; 7: 43041. 2017.
  124. Genetic differentiation between upland and lowland populations shapes the Y-chromosomal landscape of West Asia, Balanovsky etal, Volume 136, Issue 4, pp 437?450, Human Genetics, 2017.
  125. , Sandoval etal, Annals of Human Genetics, 2016. 2016.
  126. Mitochondrial DNA diversity of present-day Aboriginal Australians and implications for human evolution in Oceania, Nagle etal, Journal of Human Genetics, 2016.
  127. New native South American Y chromosome lineages, Jota etal, J. of Hum Genetics, 2016.
  128. Genome-wide signatures of male-mediated migration shaping the Indian gene pool, GaneshPrasad ArunKumar, Tatiana V Tatarinova, Jeff Duty, Debra Rollo, Adhikarla Syama, Varatharajan Santhakumari Arun, Valampuri John Kavitha, Petr Triska, Bennett Greenspan, R Spencer Wells, Ramasamy Pitchappan and The Genographic Consortium, Journal of Human Genetics , (21 May 2015) | doi:10.1038/jhg.2015.51
  129. Genetic Diversity in the Lesser Antilles and Its Implications for the Settlement of the Caribbean Basin, Torres etal, PLOS One, 2015.
  130. Antiquity and diversity of aboriginal Australian Y-chromosomes, Nagle etal, Am J Phys Anthropol. (2015).
  131. Genetic Heritage of the Balto-Slavic Speaking Populations: A Synthesis of Autosomal, Mitochondrial and Y-Chromosomal Data, Kushniarevich etal, PLOS One, 2015.
  132. Genetic diversity in Puerto Rico and its implications for the peopling of the Island and the West Indies, Vilar etal, 155(3), Ame. J. of Physical Anthropology, 2014.
  133. Geographic population structure analysis of worldwide human populations infers their biogeographical origins, Eran Elhaik, Tatiana Tatarinova, Dmitri Chebotarev, Ignazio S. Piras, Carla Maria Calò, Antonella De Montis, Manuela Atzori, Monica Marini, Sergio Tofanelli, Paolo Francalacci, Luca Pagani, Chris Tyler-Smith, Yali Xue, Francesco Cucca, Theodore G. Schurr, Jill B. Gaieski, Carlalynne Melendez, Miguel G. Vilar, Amanda C. Owings, Rocío Gómez, The Genographic Consortium, Nature Communications 5, Article number: 3513 doi:10.1038/ncomms4513 (2014)
  134. Mitochondrial Genome Sequencing in Mesolithic North East Europe Unearths a New Sub-Clade within the Broadly Distributed Human Haplogroup C1. Der Sarkissian C, Brotherton P, Balanovsky O, Templeton JEL, Llamas B, The Genographic Consortium. PLoS ONE 9(2): e87612. doi:10.1371/journal.pone.0087612 (2014)
  135. From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes, Clarke etal, 15:68, BMC Genomics, 2014.
  136. The GenoChip: A New Tool for Genetic Anthropology, Elhaik etal, vol 5(5, )Genome Biology and Evolution 2013.
  137. Contemporary paternal genetic landscape of Polish and German populations: from early medieval Slavic expansion to post-World War II resettlements, Rebala etal, Eur J Hum Genet. 2013 Apr; 21(4): 415?422.
  138. Neolithic mitochondrial haplogroup H genomes and the genetic origins of Europeans, Paul Brotherton, Wolfgang Haak, Jennifer Templeton, Guido Brandt, Julien Soubrier, Christina Jane Adler, Stephen M. Richards, Clio Der Sarkissian, Robert Ganslmeier, Susanne Friederich, Veit Dresely, Mannis van Oven, Rosalie Kenyon, Mark B. Van der Hoek, Jonas Korlach, Khai Luong, Simon Y.W. Ho, Lluis Quintana-Murci, Doron M. Behar, Harald Meller, The Genographic Consortium, Nature Communications 4, Article number: 1764 doi:10.1038/ncomms2656, 23 April, 2013.
  139. Genetic affinity between the Kam-Sui speaking Chadong and Mulam people, DENG, Q.-Y., WANG, C.-C., WANG, X.-Q., WANG, L.-X., WANG, Z.-Y., WU, W.-J., LI, H. and the Genographic Consortium, Journal of Systematics and Evolution, 51: 263–270. doi: 10.1111/jse.12009 (2013)
  140. Ancient DNA reveals key stages in the formation of central European mitochondrial genetic diversity, Brandt etal, 342(6155), Science, 2013.
  141. Y-Chromosome and mtDNA Genetics Reveal Significant Contrasts in Affinities of Modern Middle Eastern Populations with European and African Populations, Badro DA, Douaihy B, Haber M, Youhanna SC, Salloum A, The Genographic Consortium, PLoS ONE 8(1): e54616. doi:10.1371/journal.pone.0054616 (2013)
  142. Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata, Boattini A, Martinez-Cruz B, Sarno S, Harmant C, Useli A, The Genographic Consortium, PLoS ONE 8(5): e65441. doi:10.1371/journal.pone.0065441 (2013)
  143. Late Neolithic expansion of ancient Chinese revealed by Y chromosome haplogroup O3a1c-002611. WANG, C.-C., YAN, S., QIN, Z.-D., LU, Y., DING, Q.-L., WEI, L.-H., LI, S.-L., YANG, Y.-J., JIN, L., LI, H. and the Genographic Consortium, Journal of Systematics and Evolution, 51: 280–286. doi: 10.1111/j.1759-6831.2012.00244.x (2013)
  144. Ancient DNA Reveals Prehistoric Gene-Flow from Siberia in the Complex Human Population History of North East Europe. Der Sarkissian C, Balanovsky O, Brandt G, Khartanovich V, Buzhilova A, The Genographic Consortium, PLoS Genet 9(2): e1003296. doi:10.1371/journal.pgen.1003296 (2013)
  145. The Basque Paradigm: Genetic Evidence of a Maternal Continuity in the Franco-Cantabrian Region since Pre-Neolithic Times, Behar etal, 90(3) AJHG, 2012.
  146. Y-chromosome analysis reveals genetic divergence and new founding native lineages in Athapaskan- and Eskimoan-speaking populations, Dulik etal, PNAS 109(22), 2012.
  147. Mitochondrial origin of the matrilocal Mosuo people in China, Lu etal, 23(1), The Journal of DNA Mapping, Sequencing, and Analysis, 2012.
  148. Evidence of pre-Roman tribal genetic structure in Basques from uniparentally inherited markers, Martinez-Cruz etal, Sep;29(9):2211-22, Mol Biol Evol. 2012.
  149. Afghanistan's Ethnic Groups Share a Y-Chromosomal Heritage Structured by Historical Events. Haber M, Platt DE, Ashrafian Bonab M, Youhanna SC, Soria-Hernanz DF, The Genographic Consortium, PLoS ONE 7(3): e34288. doi:10.1371/journal.pone.0034288 (2012)
  150. Positive selection on mitochondrial M7 lineages among the Gelong people in Hainan, Yang K. etal, 56, 253-256, J. of Hum Gen., 2011.
  151. Y-Chromosome Analysis in Individuals Bearing the Basarab Name of the First Dynasty of Wallachian Kings, Martinez-Cruz B, Ioana M, Calafell F, Arauna LR, Sanz P, The Genographic Consortium, PLoS ONE 7(7): e41803. doi:10.1371/journal.pone.0041803 (2012)
  152. Y-chromosome O3 Haplogroup Diversity in Sino-Tibetan Populations Reveals Two Migration Routes into the Eastern Himalayas. Annals of Human Genetics, Kang, L., Lu, Y., Wang, C., Hu, K., Chen, F., Liu, K., Li, S., Jin, L., Li, H. and The Genographic Consortium, 76: 92–99. doi: 10.1111/j.1469-1809.2011.00690.x (2012)
  153. Genetic ancestry and indigenous heritage in a Native American Descendant Community in Bermuda, Schurr etal, Ame. J. of Physical Anthropology, 2012.
  154. Multiplex single-nucleotide polymorphism typing of the human Y chromosome using TaqMan probes, Martinez-Cruz B. etal, 2:13, Investigative Genetics, 2011.
  155. Parallel Evolution of Genes and Languages in the Caucasus Region, Balanovsky etal, Molecular Biology and Evolution, Volume 28, Issue 10, 1 October 2011, Pages 2905?2920, 2011.
  156. Genetic ancestry and indigenous heritage in a Native American Descendant Community in Bermuda, Gaieski etal, Ame. J. of Physical Anthropology, 2011.
  157. An updated tree of Y-chromosome Haplogroup O and revised phylogenetic positions of mutations P164 and PK4, Shi Yan, Chuan-Chao Wang, Hui Li, Shi-Lin Li, Li Jin, and The Genographic Consortium, European Journal of Human Genetics (2011) 19, 1013–1015; doi:10.1038/ejhg.2011.64; published online 20 April 2011
  158. A new subhaplogroup of native American Y-Chromosomes from the Andes, Jota, M. S., Lacerda, D. R., Sandoval, J. R., Vieira, P. P. R., Santos-Lopes, S. S., Bisso-Machado, R., Paixão-Cortes, V. R., Revollo, S., Paz-Y-Miño, C., Fujita, R., Salzano, F. M., Bonatto, S. L., Bortolini, M. C., Santos,, F. R. and and The Genographic Consortium (2011), Am. J. Phys. Anthropol., 146: 553–559. doi: 10.1002/ajpa.21519 (2011).
  159. Migration through Bottlenecks from Southeast Asia into East Asia during Last Glacial Maximum Revealed by Y Chromosomes, Yan Lu, Lanhai Wei, Chuanchao Wang, Shilin Li, Xingqiu Huang, Li Jin,Hui Li mail, The Genographic Consortium PLoS ONE 6(8): e24282. doi:10.1371/journal.pone.0024282, 2011
  160. 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).
  161. 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).
  162. 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).
  163. 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. and Li, H. The Genographic Consortium, Am. J. Phys. Anthropol., 143: 555–569. doi: 10.1002/ajpa.21350 (2010)
  164. 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).
  165. 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).
  166. Pinghua population as an exception of Han Chinese?s coherent genetic structure, Gan R-J etal, J Hum Genet., 53(4), 303-313, 2008.
  167. 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).
  168. 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).
  169. 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).
  170. 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).
  171. 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).
  172. 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).
  173. Single Molecule Methods

  174. 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.
  175. 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.
  176. Algorithmic Complexity of Physical Mapping Problems Arising in Single Molecule Methods, Laxmi Parida, IBM Technical Report, 1998.
  177. 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.
  178. 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.
  179. 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.
  180. 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.
  181. A Model and Solution to the DNA Flipping String Problem, Davi Geiger, Laxmi Parida, Courant Inst. of Math. Sciences, NYU, TR1996-720, May 1996.
  182. 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.
  183. 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.
  184. Thesis

  185. 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.)

  186. Computer Vision

  187. 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 .
  188. 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.
  189. 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.
  190. 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.
  191. Geometric Computing

  192. 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.
  193. Computational Methods for Evaluating Swept Object Boundaries, Laxmi Parida, S.P. Mudur, 10:266-276, The Visual Computer, 1994.
  194. 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 .)
  195. 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 .)
  196. A Computational Technique for General Shape Deformations for use in Font Design, Laxmi Parida, Vol 17, No. 4, Computers & Graphics, pp. 349-356, 1993.
  197. 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 .)
  198. Social Software

  199. 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.
  200. 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.

  2. Assembly Error Detection, U.S. Serial No. CN ZL201210020103.5, Jan 6, 2016
  7. TLASSO: Transductive Lasso for High Dimensional Data Regression Problems, US Patent 9135567, Sept 15, 2015.
  11. Feature Selection for Efficient Epistasis Modeling for Phenotype Prediction, US Patent DE 102014200158, May 19, 2014.
  12. Methods and systems for reconstructing genomic common ancestors, US Patent 8700334, April 15, 2014.
  13. Methods for reconstructing evolutionary data, US Patent 8645074, Feb 14, 2014.
  14. Tunneling Junction To Distinguish Targeted DNA Segment, U.S. Serial No. 13930578, June 28, 2013.
  15. VISUAL ANALYSIS OF A PROTEIN FOLDING PROCESS, US Patent 8423339, April 16, 2013.
  16. DMRMR: Dynamic Programming Algorithm to Improve the Efficiency of mRMR, U.S. Serial No. 13/745,923, Jan 21, 2013.
  17. EMRMR: Epistasis Model based on mRMR for Phenotype Prediction, U.S. Serial No. 13/745,914, Jan 21, 2013.
  18. HMRMR: A Hill Climbing Algorithm to Improve the Accuracy of mRMR, U.S. Serial No. 13/745,909, Jan 21, 2013.
  20. Stable Genes in Comparative Transcriptomics, U.S. Serial No. US 13/713970, Dec 13, 2012.
  23. EXACT HAPLOTYPE RECONSTRUCTION OF F2 POPULATIONS, U.S. Serial No. 13/529,476, June 21, 2012.
  24. SAMPLING THE SPACE OF ANCESTRAL RECOMBINATION GRAPHS, U.S. Serial No. 13/169,824, June 27, 2011.
  26. Significance Measure of Structured Clusters, US Patent 7925447, April 12, 2011.
  29. Methods and Systems for conservative extraction of over-represented extensible motifs, US Patent 7,865,313, Jan 4, 2011
  30. Pattern Discovery Techniques for Determining Maximal Irredundant and Redundant Motifs, USPTO 20100057373, March 04, 2010.
  31. Topological Motif Discovery, US Patent 7,558,768, July 7, 2009.
  33. Apparatus, system and method for data compression using irredundant patterns, US Patent 7,479,905, Jan 20, 2009.
  36. Method and system for clustering objects and finding prime redescriptors for the clusters, USPTO 0070213957, Sept 13, 2007.
  37. Method and structure for lossy compression of continuous data with extensible motifs, U.S. Patent 7259701, August 21, 2007.
  38. System and Method for Encoding and Detecting Extensible Patterns, U.S. Patent 7203680, April 10, 2007.
  39. Method and system for protein folding trajectory analysis using patterned clusters, USPTO 20060069515, March 30, 2006.
  40. Fuzzy bi-clusters on multi-feature data, USPTO 20060184459, Aug 17, 2006.
  41. Discovering Permutation Patterns, USPTO 20050060321, March 17, 2005.
  42. Methods and Apparatus for Performing Pattern Discovery and Generation with respect to Data Sequences, U.S. Patent 6571230, May 27, 2003.
  43. Multiple Sequence Alignment System and Method, U.S. Patent 6205444B1, March 20, 2001.

Invited Talks

(See conference publications for papers presented at conferences)

  1. Data-Driven Genomics, RSG with DREAM, Keynote, , Memorial Sloan Kettering, Weill Cornell Medicine, Nov 19-21, 2017.
  2. Here and now of Genomic Medicine, Institute for Computational Biomedicine Seminar Series, Weill Cornell Medicine, Nov 7, 2017.
  3. Genomic Medicine, Innovate-Med Conference, Immunotherapy, Health Technology and Regenerative Medicine, Columbia University Medical Center, October 23, 2017.
  4. Genomic Medicine, Keynote at RECOMB, Hong Kong, May 3-7, 2017.
  5. Genomics: the grit behind the glitter, IBM Global Technical Community, April 19, 2017.
  6. The here and now of Precision Oncology, and more, Invited talk at Games Logic & Society (80th Birthday Celebration Honoring Rohit Parikh), New York, Dec 01-02, 2016.
  7. Watson for Genomics: a cognitive approach to clinical oncology, Invited talk at IJCAI, New York, July 11, 2016.
  8. Watson for Genomics: a cognitive approach to clinical oncology, Keynote at the Uncertainty in AI, New York, June 29, 2016.
  9. Combinatorics of LD, AxA Workshop, Venice, Italy June 21-24, 2016.
  10. Watson for Genomics: personalized oncology, Mt Sinai, New York June 02, 2016.
  11. Biological Sciences in the Cognitive Era, Keynote at the Dies Natalis Celebration of Wageningen University, Netherlands, March 09, 2016.
  12. Watson Genomics Analytics, IBM Precision Medicine \& Wellness, October 26, 2015.
  13. New Tools to model Dynamics of Population Evolution, Lipari School on Bioinformatics and Computational Biology, Lipari, Italy, July 19-25, 2015.
  14. Computational Genomic Problems, Smurfit Institute of Genetics, Trinity College, Dublin, Ireland, July 17, 2015.
  15. Some Genetic Tools, Teagasc, Carlow, Ireland, July 15, 2015.
  16. Discrete Computations for Population Genomics, National Institute of Biomedical Genomics, Kalyani, Kolkata, Feb 10, 2015.
  17. Consumer Genomics to Genomic Medicine: Role of Discrete Algorithms, ICDCIT, Bhubaneswar, Feb 08, 2015.
  18. Melding Combinatorics & Discrete Structures for Biological Applications, Orissa Mathematical Society, Jajpur Rd, Feb 07, 2015.
  19. Applying Discrete Methods to Population Genomics, keynote at APBC, HsinChu, Taiwan, Jan 22, 2015.
  20. Microbiomics to Population Genomics: some research topics, IBM Research, Tel Aviv, Israel, Jan 08, 2015.
  21. Combinatorics to Score Gene Clusters, Stringology, Dead Sea, Israel, Jan 04-08, 2015.
  22. Population Genomics under the lens of Random-Graphs, UC Davis, Davis, Nov 18, 2014.
  23. Population Genomics under the lens of Random-Graphs, CMU, Pittsburgh, Sept 26, 2014.
  24. Random Graphs in Population Genomics, CMS Winter Meeting (Canadian Mathematical Society) Ottawa, Dec 06-09, 2013.
  25. Genetic History of Populations: Limits to Inference, Models and Algorithms for Genome Evolution, MAGE, Cantons de l'Est, Montreal, Canada, Aug 23-26, 2013.
  26. On the path towards genomic medicine, Schloss Dagstuhl, Internationales Begegnungs und Forschungszentrum fur Informatik, Germany. Aug 19-23, 2013.
  27. Random graphs in Population Genomics, CiE , Milano, Italy, July 01, 2013.
  28. Evolution of a Computational Genomicist, Women in Computability, CiE , Milano, Italy, July 01, 2013.
  29. Making Sense of Big Data, USDA-ARS , Maryland, Feb 5-6, 2013.
  30. iXora: exact Haplotype Inferencing and Trait association, PAG XXI, San Diego, Jan 12-16, 2013.
  31. The Role Of Haplotyping In Mapping The Pod Color Trait , (with Niina Haiminen) PAG XXI, San Diego, Jan 12-16, 2013.
  32. Combinatorics of ARGs, Schloss Dagstuhl, Internationales Begegnungs und Forschungszentrum fur Informatik, Germany. July 15-20, 2012.
  33. Combinatorics: an underdog in the toolkit ?, Special Session on Challenges in Computational Biology, RECOMB, Barcelona, April 28-29, 2012.
  34. Gene synteny among cacao and other plants, (with Niina Haiminen) PAG XX, San Diego, Jan 14-18, 2012.
  35. Recombination-based genomics: a genetic variation analysis in human populations, Albert Einstein College of Medicine, Bronx, Sept 21, 2011.
  36. Recombination-based genomics: a genetic variation analysis in populations, Indiana University, Bloomington, Sept 15, 2011.
  37. The Re-combinatorics of Chromosomes, Computer Science Colloquia, Purdue University, West Lafayette, Sept 13, 2011.
  38. Entropy of a standard ARG is not very high!, Parc de Recerca Biomedica de Barcelona (PRBB), Barcelona, Spain, Feb 23, 2011.
  39. The Cacao Genome Project, (with Niina Haiminen) PAG XIX, San Diego, Jan 15-19, 2011.
  40. 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.
  41. Random Graphs and Population Genetics, Seoul National University, Seoul, Jan 10, 2011.
  42. The Re-Combinatorics of Diploids, Columbia University, Oct 20, 2010.
  43. The Re-Combinatorics of Diploids, CCMB Distinguished Lecture Series, Brown University, Sept 29, 2010.
  44. How robust are NGS whole-genome assemblies? A case study with plant genomes, (with Niina Haiminen) ECCB, Ghent, Belgium, Sept 28, 2010.
  45. Combinatorics of Recombinations in Diploids, NCBI/NIH, Bethesda, July 30, 2010.
  46. Random graphs and population genomics, Schloss Dagstuhl, Internationales Begegnungs und Forschungszentrum fur Informatik, Germany. June 06-11, 2010.
  47. Combinatorics In Recombinational Population Genomics, , keynote at ISBRA, Storrs, May 23-26, 2010.
  48. Recombinomics: Phylogenetic approach to genome-wide analysis in populations, , keynote at C* Conference on Computer Science & Software Engineering (C3S2E), Montreal, May 19-20, 2010.
  49. Graph Theory in Recombinational Population Genomics, keynote at APBC (Asia Pacific Bioinformatics Conference) Bangalore, Jan 18-22, 2010.
  50. Graph Theoretic Approaches to RECOMBINOMICS, keynote at Robert Cedergren Bioinformatics Colloquium, Université de Montreal, Nov 5-6, 2009.
  51. Graph Theory in Recombinational Population Genomics, CSE Colloquium Series, UCONN, Oct 12, 2009.
  52. RECOMBINOMICS: myth or reality ? DIMACS Workshop on Algorithmics in Human Population-Genomics, April 27--29, 2009.
  53. Combinatorial-Statistic of Genes, Department of Computer Science, Princeton University, Princeton, Feb 19, 2009.
  54. Informatics in Bioinformatics, keynote address at International Symposium on Role of IT Professionals in Bioinformatics, Regional College of Management (RCM), Bhubaneswar, Jan 7, 2009.
  55. Deep Computing in Biology, National Institute of Science Education and Research (NISER), Bhubaneswar, Jan 6, 2009.
  56. Modeling Statistical Significance of Gene Clusters, Supercomputer Education and Research Centre (SERC), Indian Institute of Science (IISc), Bangalore, Dec 30, 2008.
  57. A Case for Recombinomics, Strand Life Sciences, Bangalore, Dec 30, 2008.
  58. RECOMBINOMICS: myth or reality ?National Centre for Biological Sciences (NCBS), Bangalore, Dec 29, 2008.
  59. Mathematical Models in Recombinomics, University of Delhi, International Congress of Mathematics, New Delhi, Dec 19-20, 2008.
  60. Algorithmics in Recombinational Phylogeography, IBM T J Watson, Hawthorne, Dec 08, 2008.
  61. Algorithms in Population Genetics, NYU Women in Computing, IBM T J Watson, Nov 14, 2008.
  62. Combinatorial Statistics of Gene Clusters, Mathematical & Computational Biology Seminar, Department of Mathematics, , University of California, Berkeley, Oct 29, 2008.
  63. Are we ready for OMICS of recombinations? Data Mining for Biomedical Applications , University of Florida, Gainesville, Florida, Oct 1, 2008.
  64. 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.
  65. Exploring the Recombinant Genome for Phylogeography, Universita Delgi Studi di Padova, Padua, Italy, Sept 04, 2008.
  66. 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.
  67. Algorithms For Inferring Deep Ancestry, Innovation in Drug Discovery and Development, IBM Life Sciences Virtual Expo, April 16-17, 2008.
  68. Taming Patterns through Combinatorics in Bioinformatics, Parc de Recerca Biomedica de Barcelona (PRBB), Barcelona, March 26, 2008.
  69. Combinatorics and Statistics of Gene Clusters, ACO (Algorithms, Combinatorics and Optimizations) Seminar, School of Mathematics, Georgia Tech, Atlanta, Feb 29, 2008.
  70. 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.
  71. Combinatorics and Statistics of Gene Clusters, IBM Watson Research Math Seminar Series, Nov 9, 2007.
  72. 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.
  73. Combinatorics in Bioinformatics: Permutations and Applications, Genome Biology and Bioinformatics (GBB) Retreat, University of Toronto, Toronto, May 31, 2007.
  74. 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.
  75. Permutations in Bioinformatics, Department of Computer Science, New Jersey Institute of Technology, Newark, April 30, 2007.
  76. Some Applications of Combinatorics in Bioinformatics, Physics Seminar, The Institute of Mathematical Sciences, Chennai, Dec 29, 2006.
  77. What can Bioinformatics do for you?, Institute of Bioinformatics and Applied Biotechnology (IBAB), Bangalore, Dec 28, 2006.
  78. Permutations in Bioinformatics, Computational Insights into Biological Systems, Indian Institute of Sciences, Bangalore, Dec 26-28, 2006.
  79. Permutations in Bioinformatics, International Conference on Bioinformatics, InCoB, Delhi, December 18-20, 2006.
  80. Generalized Permutation Patterns: Theory, Algorithms & Applications, at Center for Computational Biology and Bioinformatics, Columbia University Medical Center, June 08, 2006.
  81. 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.
  82. Gapped Permutation Patterns with Bounded Length, Schloss Dagstuhl, Internationales Begegnungs und Forschungszentrum fur Informatik, Germany. May 15, 2006.
  83. A Common Framework for Mining Motifs in Diverse Data, Department of Computer Science, New Jersey Institute of Technology, Newark, April 18, 2005.
  84. 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)
  85. Combinatorics and Statistics of Motifs, IBM Haifa Research Lab, Haifa, Israel, April 4, 2005.
  86. Exploiting Patterns in Biological Data, Computer Science Distinguished Lecture Series, Arizona State University, Tempe, March 28, 2005.
  87. A Uniform Framework for Studying Patterns in Data, National University of Singapore, Singapore, Jan 20, 2005.
  88. Unusual Motifs in Biological Data, Computer Science & Engineering Colloquia Series, Michigan State University, East Lansing, Nov 15, 2004.
  89. Discovering Patterns for Understanding Biological Data, New York Academy of Sciences, Nov 10, 2004.
  90. Exploiting Regularities in Biological Data, Computer Science Colloquium, City University of New York, October 7, 2004.
  91. 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.
  92. Permutation and Other Motifs, School of Computer Science, Tata Institute of Fundamental Research, Mumbai, Sept 3, 2004.
  93. Towards Understanding Large Volume Biological Data, tutorial at Utkal University, Bhubaneswar, August 30, 2004.
  94. 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.
  95. Understanding Biological Data Through Patterns, Seminar series, Othmer Institute for Interdisciplinary Studies, Polytechnic University, New York, May 19, 2004.
  96. On the Problem of Extensible Substring Patterns, General Theory of Information Transfer and Combinatorics, Zentrum fur interdisziplinare Forschung, Bielefeld, Germany, April 26-30, 2004.
  97. Permutation Motifs in Biological Data, Bioinformatics Symposium, The Center for Advanced Computer Studies, University of Louisiana, Lafayette, April 8, 2004.
  98. Permutation Patterns, Departement d'Informatique et de Recherche Operationnelle, (Laboratoire de Biologie informatique et Theorique), Unversite de Montreal, Montreal, Feb 5-6, 2004.
  99. Exploiting Regularities in Data for Bioinformatics, Computer Science and Information Technology, RMIT University, Melbourne, Australia, July 4, 2003.
  100. Flexible Pattern Discovery based on Inexact-Suffix Trees, Zentrum fur interdisziplinare Forschung, Bielefeld, Germany, February 18-20, 2003.
  101. 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)
  102. Bioinformatics and Pattern Discovery , University of Maryland, College Park, April 29, 2002.
  103. Bioinformatics and Pattern Discovery , Yale University, New Haven, April 9, 2002.
  104. Bioinformatics and Pattern Discovery , Johns Hopkins University, Baltimore, March 15, 2002.
  105. Computational Biology and Pattern Discovery , Theory Day 2001, New York, November 16, 2001.
  106. Discovering Information from Data , WORDS 2001, Palermo, September 17-21, 2001.
  107. The Role of Algorithms in Bioinformatics, Biofuture 2001, Toronto, September 5-7, 2001.
  108. Pattern Discovery and Applications, Sequence Analysis and Annotation, Symposium on Computational Genetics , Cleveland, October 20, 2000.
  109. Flexible Pattern Discovery , Summer School at the Eleventh Annual Symposium on Combinatorial Pattern Matching, Montreal, June 19-20, 2000.
  110. 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.
  111. 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.
  112. Pattern Discovery: Theory and Practice, Workshop on Knowledge Management: Moving from Business to Technical and Scientific Domains, CASCON, Toronto, Canada, November 9, 1999.
  113. Mulitple Sequence Alignment using MUSCA , Columbia Genome Center, Columbia University , New York, October 15, 1999.
  114. Motif Discovery and Applications, Computer Science Colloquium, Graduate School and University Center, City University of New York, May 25, 1999.
  115. An Algorithm for Multiple Sequence Alignment, IBM India Research Laboratory, New Delhi, April 23, 1999.
  116. Theoretical Issues in Single Molecule Methods, Department of Computer Science, University of Auckland, Auckland, January 14, 1999.
  117. Problem of Physical Mapping in Single Molecule Methods, Department of Information Science, University of Tokyo, Tokyo, December 11, 1998.
  118. Algorithmic Issues in Computational Genomics, IBM Thomas J Watson Research Center, March 19, 1998.
  119. Algorithmic Issues in Computational Genomics, Department of Computer Science, University of Georgia, Athens, March 17, 1998.
  120. Algorithmic Issues in Computational Genomics, Department of Mathematical and Computer Sciences, Loyola University Chicago, Chicago, March 13, 1998.
  121. Algorithmic Issues in Computational Genomics, Department of Computer Science, University of Iowa, Iowa City, March 9, 1998.
  122. Algorithmic Issues in Computational Genomics, Department of Computer Science, State University of New York Stony Brook, March 4, 1998.
  123. Algorithms for Single Molecule Methods , Department of Computer Science, SUNY Brockport, Brockport, February 23, 1998.

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