Predicting V(D)J Recombination Using Conditional Random Fields. - Raunaq Malhotra; Shruthi Prabhakara; Raj Acharya (PRIB, 2012)

Estimating Viral Haplotypes in a Population Using k-mer Counting. - Raunaq Malhotra; Shruthi Prabhakara; Mary Poss; Raj Acharya (PRIB, 2013)

Mutant-Bin: Unsupervised Haplotype Estimation of Viral Population Diversity Without Reference Genome. - Shruthi Prabhakara; Raunaq Malhotra; Raj Acharya; Mary Poss (J. Comput. Biol., 2013)

Computational and Statistical Analyses of Insertional Polymorphic Endogenous Retroviruses in a Non-Model Organism. - Le Bao; Daniel Elleder; Raunaq Malhotra; Michael Degiorgio; Theodora Maravegias; Lindsay Horvath; Laura Carrel; Colin Gillin; Tomás Hron; Helena Fábryová; David R. Hunter; Mary Poss (Comput., 2014)

A generalized lattice model for clustering metagenomic sequences. - Manjari Mukhopadhyay; Raunaq Malhotra; Raj Acharya (BCB, 2015)

Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data. - Yang Liu; Francesca Chiaromonte; Howard Ross; Raunaq Malhotra; Daniel Elleder; Mary Poss (BMC Bioinform., 2015)

A Generalized Lattice Based Probabilistic Approach for Metagenomic Clustering. - Manjari Jha; Raunaq Malhotra; Raj Acharya (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

QuagmiR: a cloud-based application for isomiR big data analytics. - Xavier Bofill-De Ros; Kevin Chen 004; Susanna Chen; Nikola Tesic; Dusan Randjelovic; Nikola Skundric; Svetozar Nesic; Vojislav Varjacic; Elizabeth H. Williams; Raunaq Malhotra; Minjie Jiang; Shuo Gu (Bioinform., 2019)

A computational framework to assess genome-wide distribution of polymorphic human endogenous retrovirus-K In human populations. - Weiling Li; Lin Lin 003; Raunaq Malhotra; Lei Yang 038; Raj Acharya; Mary Poss (PLoS Comput. Biol., 2019)

ViPRA-Haplo: De Novo Reconstruction of Viral Populations Using Paired End Sequencing Data. - Weiling Li; Raunaq Malhotra; Steven H. Wu; Manjari Jha; Allen G. Rodrigo; Mary Poss; Raj Acharya (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)