John Stephen Malamon

DNA N-gram Analysis Framework (DNAnamer): A generalized N-gram frequency analysis framework for the supervised classification of DNA sequences

DNAnamer is a framework that uses N-gram frequency analysis to classify DNA sequences, identifying species, functional elements, and contamination.

Structural Variation Detection and Association Analysis of Whole-Genome-Sequence Data from 16,905 Alzheimer's Diseases Sequencing Project Subjects

The paper identifies structural variations in whole-genome sequencing data from 16,905 ADSP subjects and finds associations with Alzheimer's disease and related endophenotypes.

FACTORs: a Novel R Package for Functional Data Reduction and Hypothesis Testing

FACTORs provides a method to validate differentially expressed genes across studies and reduce Type I error in functional analysis.

A comparative study of structural variant calling strategies using the Alzheimer's Disease Sequencing Project's whole genome family data

The paper evaluates deletion calling accuracy using two pipelines on ADSP whole genome family data, finding Scalpel better for small deletions and Parliament for larger ones, with 78.1% of predicted deletions validated by Sanger sequencing.

Quality Control and Integration of Genotypes from Two Calling Pipelines for Whole Genome Sequence Data in the Alzheimer’s Disease Sequencing Project

The paper describes the quality control and integration of genotype calls from two pipelines for whole genome sequencing data in the Alzheimer’s Disease Sequencing Project, resulting in a high-quality consensus dataset.

Meta-analysis of genetic association with diagnosed Alzheimer’s disease identifies novel risk loci and implicates Abeta, Tau, immunity and lipid processing

This study performs a large GWAS of Alzheimer's disease, identifies four new risk loci, and highlights pathways involving immunity, lipid metabolism, and APP/Aβ processing.