Laxmi Parida

Quantum Convolutional HLA Immunogenic Peptide Prediction (Q-CHIPP): Next-Generation Neoantigen Prediction with Quantum Neural Networks

This paper introduces Q-CHIPP, a quantum neural network for predicting HLA immunogenic peptides, combining MHC binding and immunogenicity prediction using quantum hardware.

A Multimodal Foundation Model for Discovering Genetic Associations with Brain Imaging Phenotypes

COMICAL discovers genetic associations with brain imaging phenotypes using contrastive learning and multi-omics data from the UK Biobank.

MaSk-LMM: A Matrix Sketching Framework for Linear Mixed Models in Association Studies

MaSk-LMM uses matrix sketching to efficiently estimate LMM parameters in GWAS, providing fast and accurate results compared to existing methods.

FairPRS: a fairness framework for Polygenic Risk Scores

This paper introduces FairPRS, a method to create polygenic risk scores that are fair across ethnic groups by using invariant risk minimization, showing improved phenotype prediction and reduced racial bias.

A Common Methodological Phylogenomics Framework for intra-patient heteroplasmies to infer SARS-CoV-2 sublineages and tumor clones

The paper introduces a phylogenomics framework to infer SARS-CoV-2 sublineages and tumor clones from genomic data by analyzing variant frequencies and applying a computational method called Concerti.

CuNA: Cumulant-based Network Analysis of genotype-phenotype associations in Parkinson's Disease

CuNA identifies genes associated with Parkinson's Disease symptoms by analyzing higher-order relationships between eQTLs and clinical phenotypes.

Challenges in Benchmarking Metagenomic Profilers

This paper highlights challenges in benchmarking metagenomic profilers due to confusion between sequence abundance and taxonomic abundance.

Multiple Loci Selection with Multi-way Epistasis in Coalescence with Recombination

The paper introduces EpiSimRA, a coalescent model with multi-way epistasis, validated by a forward Wright-Fisher model, showing superior performance in simulating evolutionary scenarios with selection and recombination.

Functional profiling of COVID-19 respiratory tract microbiomes

The paper analyzes RNA sequencing data from respiratory tract samples to identify functional differences in microbiomes between COVID-19 patients, pneumonia patients, and healthy controls.

EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets

EMPress provides an interactive tool for visualizing phylogenetic trees alongside multi-omic data, enabling exploratory analyses of microbiome and metabolome datasets.

Explainable AI reveals changes in skin microbiome compositionlinked to phenotypic differences

The paper develops an explainable AI approach to predict skin-related phenotypes from leg skin microbiome data and identifies microbial composition changes linked to these traits.

Integrating linguistics, social structure, and geography to model genetic diversity within India

The paper models genetic diversity in India by integrating geography, language, and social structure, finding language and social factors most influential in shaping genetic patterns.

Haplotype assembly of autotetraploid potato using integer linear programming

This paper develops an integer linear programming method for haplotype assembly in autotetraploid potato, showing improved accuracy over existing methods on both simulated and real data.