A closed form solution to the problem of tangential circles, lines, points with extension to 3D. - Laxmi Parida; Pramod Koparkar (Comput. Graph., 1991)

Vinyas: An Interactive Calligraphic Type Design System. - Laxmi Parida (ICCG, 1993)

Constraint-satisfying planar development of complex surfaces. - Laxmi Parida; Sudhir P. Mudur (Comput. Aided Des., 1993)

A computational technique for general shape deformations for use in font design. - Laxmi Parida (Comput. Graph., 1993)

Computational methods for evaluating swept object boundaries. - Laxmi Parida; Sudhir P. Mudur (Vis. Comput., 1994)

Common tangents to planar parametric curves: a geometric solution. - Laxmi Parida; Sudhir P. Mudur (Comput. Aided Des., 1995)

Visual Organization for Figure/Ground Separation. - Davi Geiger; Krishnan Kumaran; Laxmi Parida (CVPR, 1996)

Kona: A Multi-junction Detector Using Minimum Description Length Principle. - Laxmi Parida; Davi Geiger; Robert A. Hummel (EMMCVPR, 1997)

Towards constructing physical maps by optical mapping (extended abstract): an effective, simple, combinatorial approach. - S. Muthukrishnan 001; Laxmi Parida (RECOMB, 1997)

Partitioning K clones: hardness results and practical algorithms for the K-populations problem. - Laxmi Parida; Bud Mishra (RECOMB, 1998)

A Uniform Framework for Ordered Restriction Map Problems. - Laxmi Parida (J. Comput. Biol., 1998)

Junctions: Detection, Classification, and Reconstruction. - Laxmi Parida; Davi Geiger; Robert A. Hummel (IEEE Trans. Pattern Anal. Mach. Intell., 1998)

Algorithmic Techniques in Computational Genomics. - Laxmi Parida (1998)

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; Laxmi Parida (ISMB, 1999)

Sequence homology detection through large scale pattern discovery. - Aris Floratos; Isidore Rigoutsos; Laxmi Parida; Gustavo Stolovitzky; Yuan Gao (RECOMB, 1999)

Mass Estimation of DNA Molecules and Extraction of Ordered Restriction Maps in Optical Mapping Imagery. - Laxmi Parida; Dan Geiger (Algorithmica, 1999)

An Approximation Algorithm for Alignment of Multiple Sequences using Motif Discovery. - Laxmi Parida; Aris Floratos; Isidore Rigoutsos (J. Comb. Optim., 1999)

Some Results on Flexible-Pattern Discovery. - Laxmi Parida (CPM, 2000)

Pattern discovery on character sets and real-valued data: linear bound on irredundant motifs and an efficient polynomial time algorithm. - Laxmi Parida; Isidore Rigoutsos; Aris Floratos; Daniel E. Platt; Yuan Gao (SODA, 2000)

Partitioning single-molecule maps into multiple populations: algorithms and probabilistic analysis. - Laxmi Parida; Bud Mishra (Discret. Appl. Math., 2000)

An Output-Sensitive Flexible Pattern Discovery Algorithm. - Laxmi Parida; Isidore Rigoutsos; Daniel E. Platt (CPM, 2001)

DELPHI: A pattern-based method for detecting sequence similarity. - Aris Floratos; Isidore Rigoutsos; Laxmi Parida; Yuan Gao (IBM J. Res. Dev., 2001)

QSAR in grossly underdetermined systems: Opportunities and issues. - Daniel E. Platt; Laxmi Parida; Yuan Gao; Aris Floratos; Isidore Rigoutsos (IBM J. Res. Dev., 2001)

Sock Sorting: An Example of a Vague Algorithm. - Rohit Parikh; Laxmi Parida; Vaughan R. Pratt (Log. J. IGPL, 2001)

Compression and the Wheel of Fortune. - Alberto Apostolico; Laxmi Parida (DCC, 2003)

A Combinatorial Approach to Automatic Discovery of Cluster-Patterns. - Revital Eres; Gad M. Landau; Laxmi Parida (WABI, 2003)

The web server of IBM's Bioinformatics and Pattern Discovery group. - Tien Huynh; Isidore Rigoutsos; Laxmi Parida; Daniel E. Platt; Tetsuo Shibuya (Nucleic Acids Res., 2003)

Motifs in Ziv-Lempel-Welch Clef. - Alberto Apostolico; Matteo Comin; Laxmi Parida (Data Compression Conference, 2004)

Incremental Paradigms of Motif Discovery. - Alberto Apostolico; Laxmi Parida (J. Comput. Biol., 2004)

Permutation Pattern Discovery in Biosequences. - Revital Eres; Gad M. Landau; Laxmi Parida (J. Comput. Biol., 2004)

Redescription Mining: Structure Theory and Algorithms. - Laxmi Parida; Naren Ramakrishnan (AAAI, 2005)

Protein folding trajectory analysis using patterned clusters. - J. Feng; Laxmi Parida; Ruhong Zhou (APBC, 2005)

Using PQ Trees for Comparative Genomics. - Gad M. Landau; Laxmi Parida; Oren Weimann (CPM, 2005)

Off-Line Compression by Extensible Motifs. - Alberto Apostolico; Matteo Comin; Laxmi Parida (DCC, 2005)

Conservative extraction of over-represented extensible motifs. - Alberto Apostolico; Matteo Comin; Laxmi Parida (ISMB (Supplement of Bioinformatics), 2005)

Bridging Lossy and Lossless Compression by Motif Pattern Discovery. - Alberto Apostolico; Matteo Comin; Laxmi Parida (Electron. Notes Discret. Math., 2005)

Gene Proximity Analysis across Whole Genomes via PQ Trees1. - Gad M. Landau; Laxmi Parida; Oren Weimann (J. Comput. Biol., 2005)

Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a β-Hairpin. - Laxmi Parida; Ruhong Zhou (PLoS Comput. Biol., 2005)

An inexact-suffix-tree-based algorithm for detecting extensible patterns. - Abhijit Chattaraj; Laxmi Parida (Theor. Comput. Sci., 2005)

Malware phylogeny generation using permutations of code. - Md. Enamul Karim; Andrew Walenstein; Arun Lakhotia; Laxmi Parida (J. Comput. Virol., 2005)

Constructing Near-Perfect Phylogenies with multiple homoplasy events. - Ravi Vijaya Satya; Amar Mukherjee; Gabriela Alexe; Laxmi Parida; Gyan Bhanot (ISMB (Supplement of Bioinformatics), 2006)

Using Permutation Patterns for Content-Based Phylogeny. - Md. Enamul Karim; Laxmi Parida; Arun Lakhotia (PRIB, 2006)

A PQ Framework for Reconstructions of Common Ancestors and Phylogeny. - Laxmi Parida (Comparative Genomics, 2006)

Inferring Common Origins from mtDNA. - Ajay K. Royyuru; Gabriela Alexe; Daniel E. Platt; Ravi Vijaya Satya; Laxmi Parida; Saharon Rosset; Gyan Bhanot (RECOMB, 2006)

Gapped Permutation Patterns for Comparative Genomics. - Laxmi Parida (WABI, 2006)

Mining, compressing and classifying with extensible motifs. - Alberto Apostolico; Matteo Comin; Laxmi Parida (Algorithms Mol. Biol., 2006)

Using PQ Structures for Genomic Rearrangement Phylogeny. - Laxmi Parida (J. Comput. Biol., 2006)

Subtle Motif Discovery for Detection of DNA Regulatory Sites. - Matteo Comin; Laxmi Parida (APBC, 2007)

PROTERAN: animated terrain evolution for visual analysis of patterns in protein folding trajectory. - Ruhong Zhou; Laxmi Parida; Kush Kapila; Sudhir P. Mudur (Bioinform., 2007)

Gapped Permutation Pattern Discovery for Gene Order Comparisons. - Laxmi Parida (J. Comput. Biol., 2007)

Discovering Topological Motifs Using a Compact Notation. - Laxmi Parida (J. Comput. Biol., 2007)

Statistical Significance of Large Gene Clusters. - Laxmi Parida (J. Comput. Biol., 2007)

Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns. - Laxmi Parida; Marta Melé; Francesc Calafell; Jaume Bertranpetit (J. Comput. Biol., 2008)

Motif patterns in 2D. - Alberto Apostolico; Laxmi Parida; Simona E. Rombo (Theor. Comput. Sci., 2008)

Detection of subtle variations as consensus motifs. - Matteo Comin; Laxmi Parida (Theor. Comput. Sci., 2008)

Minimizing recombinations in consensus networks for phylogeographic studies. - Laxmi Parida; Asif Javed; Marta Melé; Francesc Calafell; Jaume Bertranpetit (BMC Bioinform., 2009)

Recombinomics: population genomics from a recombination perspective. - Asif Javed; Laxmi Parida (C3S2E, 2010)

10231 Abstracts Collection - Structure Discovery in Biology: Motifs, Networks & Phylogenies. - Alberto Apostolico; Andreas W. M. Dress; Laxmi Parida (Structure Discovery in Biology: Motifs, Networks & Phylogenies, 2010)

Combinatorics in Recombinational Population Genomics. - Laxmi Parida (ISBRA, 2010)

APBC 2010. The Eighth Asia Pacific Bioinformatics Conference Bangalore, India, 18-21 January 2010. - Laxmi Parida; Gene Myers (BMC Bioinform., 2010)

Ancestral Recombinations Graph: A Reconstructability Perspective Using Random-Graphs Framework. - Laxmi Parida (J. Comput. Biol., 2010)

A New Method to Reconstruct Recombination Events at a Genomic Scale. - Marta Melé; Asif Javed; Marc Pybus; Francesc Calafell; Laxmi Parida; Jaume Bertranpetit (PLoS Comput. Biol., 2010)

VARUN: Discovering Extensible Motifs under Saturation Constraints. - Alberto Apostolico; Matteo Comin; Laxmi Parida (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

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 (KDD, 2011)

IRiS: Construction of ARG networks at genomic scales. - Asif Javed; Marc Pybus; Marta Melé; Filippo Utro; Jaume Bertranpetit; Francesc Calafell; Laxmi Parida (Bioinform., 2011)

A minimal descriptor of an ancestral recombinations graph. - Laxmi Parida; Pier Francesco Palamara; Asif Javed (BMC Bioinform., 2011)

Characterization and Extraction of Irredundant Tandem Motifs. - Laxmi Parida; Cinzia Pizzi; Simona E. Rombo (SPIRE, 2012)

ARG-based genome-wide analysis of cacao cultivars. - Filippo Utro; Omar Cornejo; Donald Livingstone; Juan Motamayor; Laxmi Parida (BMC Bioinform., 2012)

Structure Discovery in Biology: Motifs, Networks & Phylogenies (Dagstuhl Seminar 12291). - Alberto Apostolico; Andreas W. M. Dress; Laxmi Parida (Dagstuhl Reports, 2012)

Combinatorial Pattern Matching (CPM 2010). - Amihood Amir; Laxmi Parida (Inf. Comput., 2012)

Genetic History of Populations: Limits to Inference. - Daniel E. Platt; Filippo Utro; Marc Pybus; Laxmi Parida (Models and Algorithms for Genome Evolution, 2013)

Using Random Graphs in Population Genomics. - Laxmi Parida (CiE, 2013)

Efficient in silico Chromosomal Representation of Populations via Indexing Ancestral Genomes. - Niina Haiminen; Filippo Utro; Claude Lebreton; Pascal Flament; Zivan Karaman; Laxmi Parida (Algorithms, 2013)

Ultrametric networks: a new tool for phylogenetic analysis. - Alberto Apostolico; Matteo Comin; Andreas W. M. Dress; Laxmi Parida (Algorithms Mol. Biol., 2013)

Sum of parts is greater than the whole: inference of common genetic history of populations. - Filippo Utro; Marc Pybus; Laxmi Parida (BMC Genom., 2013)

Spectral Sequences, Exact Couples and Persistent Homology of filtrations. - Saugata Basu; Laxmi Parida (CoRR, 2013)

MINT: Mutual Information based Transductive Feature Selection for Genetic Trait Prediction. - Dan He 001; Irina Rish; David Haws; Simon Teyssedre; Zivan Karaman; Laxmi Parida (CoRR, 2013)

ICT for Bridging Biology and Medicine (Dagstuhl Perspectives Workshop 13342). - Jonas S. Almeida; Andreas W. M. Dress; Titus Kühne; Laxmi Parida (Dagstuhl Manifestos, 2013)

ICT Strategies for Bridging Biology and Precision Medicine (Dagstuhl Perspectives Workshop 13342). - Jonas S. Almeida; Andreas W. M. Dress; Titus Kühne; Laxmi Parida (Dagstuhl Reports, 2013)

IPED: Inheritance Path-based Pedigree Reconstruction Algorithm Using Genotype Data. - Dan He 001; Zhanyong Wang; Buhm Han; Laxmi Parida; Eleazar Eskin (J. Comput. Biol., 2013)

Transductive HSIC Lasso. - Dan He 001; Irina Rish; Laxmi Parida (SDM, 2014)

Best-Fit in Linear Time for Non-generative Population Simulation - (Extended Abstract). - Niina Haiminen; Claude Lebreton; Laxmi Parida (WABI, 2014)

Entropic Profiles, Maximal Motifs and the Discovery of Significant Repetitions in Genomic Sequences. - Laxmi Parida; Cinzia Pizzi; Simona E. Rombo (WABI, 2014)

Effect of sampling on the extent and accuracy of the inferred genetic history of recombining genome. - Daniel E. Platt; Filippo Utro; Laxmi Parida (Comput. Biol. Chem., 2014)

Irredundant tandem motifs. - Laxmi Parida; Cinzia Pizzi; Simona E. Rombo (Theor. Comput. Sci., 2014)

SAME: a sampling-based multi-locus epistasis algorithm for quantitative genetic trait prediction. - Dan He 001; Laxmi Parida (BCB, 2015)

Performance evaluation of different encoding strategies for quantitative genetic trait prediction. - Oyetunji E. Ogundijo; Dan He 001; Laxmi Parida (ICCABS, 2015)

Host Trait Prediction of Metagenomic Data for Topology-Based Visualization. - Laxmi Parida; Niina Haiminen; David Haws; Jan Suchodolski (ICDCIT, 2015)

MINED: An Efficient Mutual Information Based Epistasis Detection Method to Improve Quantitative Genetic Trait Prediction. - Dan He 001; Zhanyong Wang; Laxmi Parida (ISBRA, 2015)

Topological Signatures for Population Admixture. - Laxmi Parida; Filippo Utro; Deniz Yörükoglu; Anna Paola Carrieri; David Kuhn; Saugata Basu (RECOMB, 2015)

SimBA: simulation algorithm to fit extant-population distributions. - Laxmi Parida; Niina Haiminen (BMC Bioinform., 2015)

Data-driven encoding for quantitative genetic trait prediction. - Dan He 001; Zhanyong Wang; Laxmi Parida (BMC Bioinform., 2015)

Scalable Algorithms at Genomic Resolution to fit LD Distributions. - Laxmi Parida; Niina Haiminen (BCB, 2016)

Host Phenotype Prediction from Differentially Abundant Microbes Using RoDEO. - Anna Paola Carrieri; Niina Haiminen; Laxmi Parida (CIBB, 2016)

Sampling ARG of multiple populations under complex configurations of subdivision and admixture. - Anna Paola Carrieri; Filippo Utro; Laxmi Parida (Bioinform., 2016)

Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction. - Dan He 001; David Kuhn; Laxmi Parida (Bioinform., 2016)

Does encoding matter? A novel view on the quantitative genetic trait prediction problem. - Dan He 001; Laxmi Parida (BMC Bioinform., 2016)

Characterizing redescriptions using persistent homology to isolate genetic pathways contributing to pathogenesis. - Daniel E. Platt; Saugata Basu; Pierre A. Zalloua; Laxmi Parida (BMC Syst. Biol., 2016)

Design of the MCAW compute service for food safety bioinformatics. - Stefan Edlund; Kristen L. Beck; Niina Haiminen; Laxmi Parida; Brian D. Storey; Bart C. Weimer; James H. Kaufman; David D. Chambliss (IBM J. Res. Dev., 2016)

MINT: Mutual Information Based Transductive Feature Selection for Genetic Trait Prediction. - Dan He 001; Irina Rish; David Haws; Laxmi Parida (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

A Quantitative and Qualitative Characterization of k-mer Based Alignment-Free Phylogeny Construction. - Filippo Utro; Daniel E. Platt; Laxmi Parida (CIBB, 2017)

MUSE: A Multi-locus Sampling-based Epistasis Algorithm for Quantitative Genetic Trait Prediction. - Dan He 001; Laxmi Parida (PSB, 2017)

IPED2: Inheritance Path Based Pedigree Reconstruction Algorithm for Complicated Pedigrees. - Dan He 001; Zhanyong Wang; Laxmi Parida; Eleazar Eskin (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Simultaneous Phasing of Multiple Polyploids. - Laxmi Parida; Filippo Utro (CIBB, 2018)

Essential Simplices in Persistent Homology and Subtle Admixture Detection. - Saugata Basu; Filippo Utro; Laxmi Parida (WABI, 2018)

Efficient algorithms for polyploid haplotype phasing. - Dan He 001; Subrata Saha; Richard Finkers; Laxmi Parida (BMC Genom., 2018)

Efficient Algorithms for Sequence Analysis with Entropic Profiles. - Cinzia Pizzi; Mattia Ornamenti; Simone Spangaro; Simona E. Rombo; Laxmi Parida (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Haplotype assembly of autotetraploid potato using integer linear programing. - Enrico Siragusa; Niina Haiminen; Richard Finkers; Richard G. F. Visser; Laxmi Parida (Bioinform., 2019)

Signal enrichment with strain-level resolution in metagenomes using topological data analysis. - Aldo Guzmán-Sáenz; Niina Haiminen; Saugata Basu; Laxmi Parida (BMC Genom., 2019)

Dark-matter matters: Discriminating subtle blood cancers using the darkest DNA. - Laxmi Parida; Claudia Haferlach; Kahn Rhrissorrakrai; Filippo Utro; Chaya Levovitz; Wolfgang Kern; Niroshan Nadarajah; Sven Twardziok; Stephan Hutter; Manja Meggendorfer; Wencke Walter; Constance Baer; et al. (PLoS Comput. Biol., 2019)

Linear Time Algorithms to Construct Populations Fitting Multiple Constraint Distributions at Genomic Scales. - Enrico Siragusa; Niina Haiminen; Filippo Utro; Laxmi Parida (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

A Topological Data Analysis Approach on Predicting Phenotypes from Gene Expression Data. - Sayan Mandal; Aldo Guzmán-Sáenz; Niina Haiminen; Saugata Basu; Laxmi Parida (AlCoB, 2020)

Utilizing stability criteria in choosing feature selection methods yields reproducible results in microbiome data. - Lingjing Jiang; Niina Haiminen; Anna Paola Carrieri; Shi Huang; Yoshiki Vazquez-Baeza; Laxmi Parida; Ho-Cheol Kim; Austin D. Swafford; Rob Knight 001; Loki Natarajan (CoRR, 2020)

Impact of Clinical and Genomic Factors on COVID-19 Disease Severity. - Sanjoy Dey; Aritra Bose; Subrata Saha; Prithwish Chakraborty; Mohamed F. Ghalwash; Filippo Utro; Aldo Guzmán-Sáenz; Kenney Ng; Jianying Hu; Laxmi Parida; Daby Sow (AMIA, 2021)

Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination. - Aritra Bose; Filippo Utro; Daniel E. Platt; Laxmi Parida (Algorithms, 2021)

Inferring COVID-19 Biological Pathways from Clinical Phenotypes via Topological Analysis. - Negin Karisani; Daniel E. Platt; Saugata Basu; Laxmi Parida (CoRR, 2021)

Sequents, barcodes, and homology. - Saugata Basu; Negin Karisani; Laxmi Parida (CoRR, 2022)

Quantum Analog of Shannon's Lower Bound Theorem. - Saugata Basu; Laxmi Parida (CoRR, 2023)

Lesion Shedding Model: unraveling site-specific contributions to ctDNA. - Kahn Rhrissorrakrai; Filippo Utro; Chaya Levovitz; Laxmi Parida (Briefings Bioinform., 2023)

Hybrid Quantum-Classical Graph Neural Networks for Tumor Classification in Digital Pathology. - Anupama Ray; Dhiraj Madan; Srushti Patil; Pushpak Pati; Maria Anna Rapsomaniki; Aviwe Kohlakala; Thembelihle Rose Dlamini; Stephanie Julia Muller; Kahn Rhrissorrakrai; Filippo Utro; Laxmi Parida (QCE, 2024)

MaSk-LMM: A Matrix Sketching Framework for Linear Mixed Models in Association Studies. - Myson C. Burch; Aritra Bose; Gregory Dexter; Laxmi Parida; Petros Drineas (RECOMB, 2024)

AutoXAI4Omics: an automated explainable AI tool for omics and tabular data. - James Strudwick; Laura-Jayne Gardiner; Kate Denning-James; Niina Haiminen; Ashley Evans; Jennifer Kelly; Matthew Madgwick; Filippo Utro; Ed Seabolt; Christopher Gibson; Bharat Bedi; Daniel Clayton; et al. (Briefings Bioinform., 2024)

Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions. - Daniel E. Platt; Aritra Bose; Kahn Rhrissorrakrai; Chaya Levovitz; Laxmi Parida (Bioinform., 2024)

Towards quantum computing for clinical trial design and optimization: A perspective on new opportunities and challenges. - Hakan Doga; Mustafa Emre Sahin; Joao H. Bettencourt-Silva; Anh Pham; Eunyoung Kim; Alan Andress; Sudhir Saxena; Aritra Bose; Laxmi Parida; Jan Lukas Robertus; Hideaki Kawaguchi; Radwa Soliman; et al. (CoRR, 2024)

How quantum computing can enhance biomarker discovery. - Frederik F. Flöther; Daniel Blankenberg; Maria Demidik; Karl Jansen; Raga Krishnakumar; Rajiv Krishnakumar; Nouamane Laanait; Laxmi Parida; Carl Y. Saab; Filippo Utro (Patterns, 2025)

Towards Quantum Tensor Decomposition in Biomedical Applications. - Myson C. Burch; Jiasen Zhang; Gideon Idumah; Hakan Doga; Richard Lartey; Lamis Yehia; Mingrui Yang; Murat Yildirim; Mihriban Karaayvaz; Omar Shehab; Weihong Guo; Ying Ni; et al. (CoRR, 2025)

Quantum Ensembling Methods for Healthcare and Life Science. - Kahn Rhrissorrakrai; Kathleen E. Hamilton; Prerana Bangalore Parthsarathy; Aldo Guzmán-Sáenz; Tyler Alban; Filippo Utro; Laxmi Parida (CoRR, 2025)

Enhanced Prediction of CAR T-Cell Cytotoxicity with Quantum-Kernel Methods. - Filippo Utro; Meltem Tolunay; Kahn Rhrissorrakrai; Tanvi P. Gujarati; Jie Shi; Sara Capponi; Mirko Amico; Nathan Earnest-Noble; Laxmi Parida (CoRR, 2025)