Laxmi Parida

According to our database, Laxmi Parida authored at least 120 papers between 1991 and 2023.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

2023

Lesion Shedding Model: unraveling site-specific contributions to ctDNA.

Kahn Rhrissorrakrai, Filippo Utro, Chaya Levovitz, Laxmi Parida

Briefings Bioinform., March, 2023

Quantum Analog of Shannon's Lower Bound Theorem.

Saugata Basu, Laxmi Parida

CoRR, 2023

2022

Sequents, barcodes, and homology.

Saugata Basu, Negin Karisani, Laxmi Parida

CoRR, 2022

Epidemiological topology data analysis links severe COVID-19 to RAAS and hyperlipidemia associated metabolic syndrome conditions.

Daniel E. Platt, Aritra Bose, Chaya Levovitz, Kahn Rhrissorrakrai, Laxmi Parida

Proceedings of the AMIA 2022, 2022

2021

Inferring COVID-19 Biological Pathways from Clinical Phenotypes via Topological Analysis.

Negin Karisani, Daniel E. Platt, Saugata Basu, Laxmi Parida

CoRR, 2021

Multiple Loci Selection with Multi-Way Epistasis in Coalescence with Recombination.

Aritra Bose, Filippo Utro, Daniel E. Platt, Laxmi Parida

Algorithms, 2021

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

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

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, Loki Natarajan

CoRR, 2020

A Topological Data Analysis Approach on Predicting Phenotypes from Gene Expression Data.

Sayan Mandal, Aldo Guzmán-Sáenz, Niina Haiminen, Saugata Basu, Laxmi Parida

Proceedings of the Algorithms for Computational Biology, 2020

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

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, Torsten Haferlach

PLoS Comput. Biol., 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

Haplotype assembly of autotetraploid potato using integer linear programing.

Enrico Siragusa, Niina Haiminen, Richard Finkers, Richard G. F. Visser, Laxmi Parida

Bioinform., 2019

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

Efficient algorithms for polyploid haplotype phasing.

Dan He, Subrata Saha, Richard Finkers, Laxmi Parida

BMC Genom., 2018

Essential Simplices in Persistent Homology and Subtle Admixture Detection.

Saugata Basu, Filippo Utro, Laxmi Parida

Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

Simultaneous Phasing of Multiple Polyploids.

Laxmi Parida, Filippo Utro

Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2018

2017

IPED2: Inheritance Path Based Pedigree Reconstruction Algorithm for Complicated Pedigrees.

Dan He, Zhanyong Wang, Laxmi Parida, Eleazar Eskin

IEEE ACM Trans. Comput. Biol. Bioinform., 2017

MUSE: A Multi-locus Sampling-based Epistasis Algorithm for Quantitative Genetic Trait Prediction.

Dan He, Laxmi Parida

Proceedings of the Biocomputing 2017: Proceedings of the Pacific Symposium, 2017

A Quantitative and Qualitative Characterization of k-mer Based Alignment-Free Phylogeny Construction.

Filippo Utro, Daniel E. Platt, Laxmi Parida

Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2017

2016

MINT: Mutual Information Based Transductive Feature Selection for Genetic Trait Prediction.

Dan He, Irina Rish, David Haws, Laxmi Parida

IEEE ACM Trans. Comput. Biol. Bioinform., 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

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

Does encoding matter? A novel view on the quantitative genetic trait prediction problem.

Dan He, Laxmi Parida

BMC Bioinform., 2016

Novel applications of multitask learning and multiple output regression to multiple genetic trait prediction.

Dan He, David Kuhn, Laxmi Parida

Bioinform., 2016

Sampling ARG of multiple populations under complex configurations of subdivision and admixture.

Anna Paola Carrieri, Filippo Utro, Laxmi Parida

Bioinform., 2016

Host Phenotype Prediction from Differentially Abundant Microbes Using RoDEO.

Anna Paola Carrieri, Niina Haiminen, Laxmi Parida

Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2016

Scalable Algorithms at Genomic Resolution to fit LD Distributions.

Laxmi Parida, Niina Haiminen

Proceedings of the 7th ACM International Conference on Bioinformatics, 2016

2015

Data-driven encoding for quantitative genetic trait prediction.

Dan He, Zhanyong Wang, Laxmi Parida

BMC Bioinform., January, 2015

SimBA: simulation algorithm to fit extant-population distributions.

Laxmi Parida, Niina Haiminen

BMC Bioinform., 2015

Topological Signatures for Population Admixture.

Laxmi Parida, Filippo Utro, Deniz Yörükoglu, Anna Paola Carrieri, David Kuhn, Saugata Basu

Proceedings of the Research in Computational Molecular Biology, 2015

MINED: An Efficient Mutual Information Based Epistasis Detection Method to Improve Quantitative Genetic Trait Prediction.

Dan He, Zhanyong Wang, Laxmi Parida

Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

Host Trait Prediction of Metagenomic Data for Topology-Based Visualization.

Laxmi Parida, Niina Haiminen, David Haws, Jan Suchodolski

Proceedings of the Distributed Computing and Internet Technology, 2015

Performance evaluation of different encoding strategies for quantitative genetic trait prediction.

Oyetunji E. Ogundijo, Dan He, Laxmi Parida

Proceedings of the 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences, 2015

SAME: a sampling-based multi-locus epistasis algorithm for quantitative genetic trait prediction.

Dan He, Laxmi Parida

Proceedings of the 6th ACM Conference on Bioinformatics, 2015

2014

Irredundant tandem motifs.

Laxmi Parida, Cinzia Pizzi, Simona E. Rombo

Theor. Comput. Sci., 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

Entropic Profiles, Maximal Motifs and the Discovery of Significant Repetitions in Genomic Sequences.

Laxmi Parida, Cinzia Pizzi, Simona E. Rombo

Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

Best-Fit in Linear Time for Non-generative Population Simulation - (Extended Abstract).

Niina Haiminen, Claude Lebreton, Laxmi Parida

Proceedings of the Algorithms in Bioinformatics - 14th International Workshop, 2014

Transductive HSIC Lasso.

Dan He, Irina Rish, Laxmi Parida

Proceedings of the 2014 SIAM International Conference on Data Mining, 2014

2013

IPED: Inheritance Path-based Pedigree Reconstruction Algorithm Using Genotype Data.

Dan He, Zhanyong Wang, Buhm Han, Laxmi Parida, Eleazar Eskin

J. Comput. Biol., 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

ICT for Bridging Biology and Medicine (Dagstuhl Perspectives Workshop 13342).

Jonas S. Almeida, Andreas W. M. Dress, Titus Kühne, Laxmi Parida

Dagstuhl Manifestos, 2013

MINT: Mutual Information based Transductive Feature Selection for Genetic Trait Prediction.

Dan He, Irina Rish, David Haws, Simon Teyssedre, Zivan Karaman, Laxmi Parida

CoRR, 2013

Spectral Sequences, Exact Couples and Persistent Homology of filtrations.

Saugata Basu, Laxmi Parida

CoRR, 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

Ultrametric networks: a new tool for phylogenetic analysis.

Alberto Apostolico, Matteo Comin, Andreas W. M. Dress, Laxmi Parida

Algorithms Mol. Biol., 2013

Efficient <i>in silico</i> Chromosomal Representation of Populations via Indexing Ancestral Genomes.

Niina Haiminen, Filippo Utro, Claude Lebreton, Pascal Flament, Zivan Karaman, Laxmi Parida

Algorithms, 2013

Using Random Graphs in Population Genomics.

Laxmi Parida

Proceedings of the Nature of Computation. Logic, Algorithms, Applications, 2013

Genetic History of Populations: Limits to Inference.

Daniel E. Platt, Filippo Utro, Marc Pybus, Laxmi Parida

Proceedings of the Models and Algorithms for Genome Evolution, 2013

2012

Combinatorial Pattern Matching (CPM 2010).

Amihood Amir, Laxmi Parida

Inf. Comput., 2012

Structure Discovery in Biology: Motifs, Networks & Phylogenies (Dagstuhl Seminar 12291).

Alberto Apostolico, Andreas W. M. Dress, Laxmi Parida

Dagstuhl Reports, 2012

ARG-based genome-wide analysis of cacao cultivars.

Filippo Utro, Omar Cornejo, Donald Livingstone, Juan Motamayor, Laxmi Parida

BMC Bioinform., 2012

Characterization and Extraction of Irredundant Tandem Motifs.

Laxmi Parida, Cinzia Pizzi, Simona E. Rombo

Proceedings of the String Processing and Information Retrieval, 2012

2011

A minimal descriptor of an ancestral recombinations graph.

Laxmi Parida, Pier Palamara, Asif Javed

BMC Bioinform., 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

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

Proceedings of the 17th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2011

2010

VARUN: Discovering Extensible Motifs under Saturation Constraints.

Alberto Apostolico, Matteo Comin, Laxmi Parida

IEEE ACM Trans. Comput. Biol. Bioinform., 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

Ancestral Recombinations Graph: A Reconstructability Perspective Using Random-Graphs Framework.

Laxmi Parida

J. Comput. Biol., 2010

APBC 2010. The Eighth Asia Pacific Bioinformatics Conference Bangalore, India, 18-21 January 2010.

Laxmi Parida, Gene Myers

BMC Bioinform., 2010

Combinatorics in Recombinational Population Genomics.

Laxmi Parida

Proceedings of the Bioinformatics Research and Applications, 6th International Symposium, 2010

10231 Abstracts Collection - Structure Discovery in Biology: Motifs, Networks & Phylogenies.

Alberto Apostolico, Andreas W. M. Dress, Laxmi Parida

Proceedings of the Structure Discovery in Biology: Motifs, Networks & Phylogenies, 06.06., 2010

<i>Recombinomics</i>: population genomics from a recombination perspective.

Asif Javed, Laxmi Parida

Proceedings of the Canadian Conference on Computer Science & Software Engineering, 2010

2009

Minimizing recombinations in consensus networks for phylogeographic studies.

Laxmi Parida, Asif Javed, Marta Melé, Francesc Calafell, Jaume Bertranpetit

BMC Bioinform., 2009

2008

Detection of subtle variations as consensus motifs.

Matteo Comin, Laxmi Parida

Theor. Comput. Sci., 2008

Motif patterns in 2D.

Alberto Apostolico, Laxmi Parida, Simona E. Rombo

Theor. Comput. Sci., 2008

Estimating the Ancestral Recombinations Graph (ARG) as Compatible Networks of SNP Patterns.

Laxmi Parida, Marta Melé, Francesc Calafell, Jaume Bertranpetit

J. Comput. Biol., 2008

2007

Statistical Significance of Large Gene Clusters.

Laxmi Parida

J. Comput. Biol., 2007

Discovering Topological Motifs Using a Compact Notation.

Laxmi Parida

J. Comput. Biol., 2007

Gapped Permutation Pattern Discovery for Gene Order Comparisons.

Laxmi Parida

J. Comput. Biol., 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

Subtle Motif Discovery for Detection of DNA Regulatory Sites.

Matteo Comin, Laxmi Parida

Proceedings of 5th Asia-Pacific Bioinformatics Conference, 2007

2006

Using PQ Structures for Genomic Rearrangement Phylogeny.

Laxmi Parida

J. Comput. Biol., 2006

Mining, compressing and classifying with extensible motifs.

Alberto Apostolico, Matteo Comin, Laxmi Parida

Algorithms Mol. Biol., 2006

Gapped Permutation Patterns for Comparative Genomics.

Laxmi Parida

Proceedings of the Algorithms in Bioinformatics, 6th International Workshop, 2006

Inferring Common Origins from mtDNA.

Ajay K. Royyuru, Gabriela Alexe, Daniel E. Platt, Ravi Vijaya Satya, Laxmi Parida, Saharon Rosset, Gyan Bhanot

Proceedings of the Research in Computational Molecular Biology, 2006

A PQ Framework for Reconstructions of Common Ancestors and Phylogeny.

Laxmi Parida

Proceedings of the Comparative Genomics, 2006

Using Permutation Patterns for Content-Based Phylogeny.

Md. Enamul Karim, Laxmi Parida, Arun Lakhotia

Proceedings of the Pattern Recognition in Bioinformatics, International Workshop, 2006

Constructing Near-Perfect Phylogenies with multiple homoplasy events.

Ravi Vijaya Satya, Amar Mukherjee, Gabriela Alexe, Laxmi Parida, Gyan Bhanot

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006

2005

Malware phylogeny generation using permutations of code.

Md. Enamul Karim, Andrew Walenstein, Arun Lakhotia, Laxmi Parida

J. Comput. Virol., 2005

An inexact-suffix-tree-based algorithm for detecting extensible patterns.

Abhijit Chattaraj, Laxmi Parida

Theor. Comput. Sci., 2005

Combinatorial Pattern Discovery Approach for the Folding Trajectory Analysis of a <i>β</i>-Hairpin.

Laxmi Parida, Ruhong Zhou

PLoS Comput. Biol., 2005

Gene Proximity Analysis across Whole Genomes via PQ Trees¹.

Gad M. Landau, Laxmi Parida, Oren Weimann

J. Comput. Biol., 2005

Bridging Lossy and Lossless Compression by Motif Pattern Discovery.

Alberto Apostolico, Matteo Comin, Laxmi Parida

Electron. Notes Discret. Math., 2005

Conservative extraction of over-represented extensible motifs.

Alberto Apostolico, Matteo Comin, Laxmi Parida

Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005

Off-Line Compression by Extensible Motifs.

Alberto Apostolico, Matteo Comin, Laxmi Parida

Proceedings of the 2005 Data Compression Conference (DCC 2005), 2005

Using PQ Trees for Comparative Genomics.

Gad M. Landau, Laxmi Parida, Oren Weimann

Proceedings of the Combinatorial Pattern Matching, 16th Annual Symposium, 2005

Protein folding trajectory analysis using patterned clusters.

J. Feng, Laxmi Parida, Ruhong Zhou

Proceedings of 3rd Asia-Pacific Bioinformatics Conference, 17-21 January 2005, Singapore, 2005

Redescription Mining: Structure Theory and Algorithms.

Laxmi Parida, Naren Ramakrishnan

Proceedings of the Proceedings, 2005

2004

Permutation Pattern Discovery in Biosequences.

Revital Eres, Gad M. Landau, Laxmi Parida

J. Comput. Biol., 2004

Incremental Paradigms of Motif Discovery.

Alberto Apostolico, Laxmi Parida

J. Comput. Biol., 2004

Motifs in Ziv-Lempel-Welch Clef.

Alberto Apostolico, Matteo Comin, Laxmi Parida

Proceedings of the 2004 Data Compression Conference (DCC 2004), 2004

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

A Combinatorial Approach to Automatic Discovery of Cluster-Patterns.

Revital Eres, Gad M. Landau, Laxmi Parida

Proceedings of the Algorithms in Bioinformatics, Third International Workshop, 2003

Compression and the Wheel of Fortune.

Alberto Apostolico, Laxmi Parida

Proceedings of the 2003 Data Compression Conference (DCC 2003), 2003

2001

Sock Sorting: An Example of a Vague Algorithm.

Rohit Parikh, Laxmi Parida, Vaughan R. Pratt

Log. J. IGPL, 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

DELPHI: A pattern-based method for detecting sequence similarity.

Aris Floratos, Isidore Rigoutsos, Laxmi Parida, Yuan Gao

IBM J. Res. Dev., 2001

An Output-Sensitive Flexible Pattern Discovery Algorithm.

Laxmi Parida, Isidore Rigoutsos, Daniel E. Platt

Proceedings of the Combinatorial Pattern Matching, 12th Annual Symposium, 2001

2000

Partitioning single-molecule maps into multiple populations: algorithms and probabilistic analysis.

Laxmi Parida, Bud Mishra

Discret. Appl. Math., 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

Proceedings of the Eleventh Annual ACM-SIAM Symposium on Discrete Algorithms, 2000

Some Results on Flexible-Pattern Discovery.

Laxmi Parida

Proceedings of the Combinatorial Pattern Matching, 11th Annual Symposium, 2000

1999

An Approximation Algorithm for Alignment of Multiple Sequences using Motif Discovery.

Laxmi Parida, Aris Floratos, Isidore Rigoutsos

J. Comb. Optim., 1999

Mass Estimation of DNA Molecules and Extraction of Ordered Restriction Maps in Optical Mapping Imagery.

Laxmi Parida, Dan Geiger

Algorithmica, 1999

Sequence homology detection through large scale pattern discovery.

Aris Floratos, Isidore Rigoutsos, Laxmi Parida, Gustavo Stolovitzky, Yuan Gao

Proceedings of the Third Annual International Conference on Research in Computational Molecular Biology, 1999

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

Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999

1998

Algorithmic Techniques in Computational Genomics.

Laxmi Parida

PhD thesis, 1998

Junctions: Detection, Classification, and Reconstruction.

Laxmi Parida, Davi Geiger, Robert A. Hummel

IEEE Trans. Pattern Anal. Mach. Intell., 1998

A Uniform Framework for Ordered Restriction Map Problems.

Laxmi Parida

J. Comput. Biol., 1998

Partitioning <i>K</i> clones: hardness results and practical algorithms for the <i>K-populations problem</i>.

Laxmi Parida, Bud Mishra

Proceedings of the Second Annual International Conference on Research in Computational Molecular Biology, 1998

1997

Towards constructing physical maps by optical mapping (extended abstract): an effective, simple, combinatorial approach.

S. Muthukrishnan, Laxmi Parida

Proceedings of the First Annual International Conference on Research in Computational Molecular Biology, 1997

Kona: A Multi-junction Detector Using Minimum Description Length Principle.

Laxmi Parida, Davi Geiger, Robert A. Hummel

Proceedings of the Energy Minimization Methods in Computer Vision and Pattern Recognition, 1997

1996

Visual Organization for Figure/Ground Separation.

Davi Geiger, Krishnan Kumaran, Laxmi Parida

Proceedings of the 1996 Conference on Computer Vision and Pattern Recognition (CVPR '96), 1996

1995

Common tangents to planar parametric curves: a geometric solution.

Laxmi Parida, Sudhir P. Mudur

Comput. Aided Des., 1995

1994

Computational methods for evaluating swept object boundaries.

Laxmi Parida, Sudhir P. Mudur

Vis. Comput., 1994

1993

A computational technique for general shape deformations for use in font design.

Laxmi Parida

Comput. Graph., 1993

Constraint-satisfying planar development of complex surfaces.

Laxmi Parida, Sudhir P. Mudur

Comput. Aided Des., 1993

Vinyas: An Interactive Calligraphic Type Design System.

Laxmi Parida

Proceedings of the Graphics, Design and Visualization, Proceedings of the IFIP TC5/WG5.2/WG5.10 CSI International Conference on Computer Graphics, 1993

1991

A closed form solution to the problem of tangential circles, lines, points with extension to 3D.

Laxmi Parida, Pramod Koparkar

Comput. Graph., 1991