12 citations · 20 across the 5 of their papers we have counts for
5 papers
A frame-based representation of genomic sequences for removing errors and rare variant detection in NGS data
Raunaq Malhotra, Manjari Mukhopadhyay, Mary Poss +1
We propose a frame-based representation of k-mers for detecting sequencing errors and rare variants in next generation sequencing data obtained from populations of closely related…
Separating Putative Pathogens from Background Contamination with Principal Orthogonal Decomposition: Evidence for Leptospira in the Ugandan Neonatal Septisome
Steven J. Schiff, Julius Kiwanuka, Gina Riggio +14
Neonatal sepsis (NS) is responsible for over a 1 million yearly deaths worldwide. In the developing world NS is often treated without an identified microbial pathogen. Amplicon seq…
Assignment of endogenous retrovirus integration sites using a mixture model
David R. Hunter, Le Bao, Mary Poss
Structural variation occurs in the genomes of individuals because of the different positions occupied by repetitive genome elements like endogenous retroviruses, or ERVs. The prese…
Maximum Likelihood de novo reconstruction of viral populations using paired end sequencing data
Raunaq Malhotra, Manjari Mukhopadhyay Steven Wu, Allen Rodrigo +2
We present MLEHaplo, a maximum likelihood de novo assembly algorithm for reconstructing viral haplotypes in a virus population from paired-end next generation sequencing (NGS) data…
Clustering pipeline for determining consensus sequences in targeted next-generation sequencing
Raunaq Malhotra, Daniel Elleder, Le Bao +3
Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a…