Niema Moshiri

This study identifies epigenetic sequence differences between endogenous and exogenous retroviral integrants using statistical analysis of public sequence data.

CompactTree is a lightweight C++ library for efficiently handling ultra-large phylogenetic trees, offering faster performance and lower memory usage than existing tools.

Reanalysis of public environmental metatranscriptomes from the Huanan market links SARS-CoV-2 positivity to one wildlife stall containing raccoon dog, civet and bamboo rat genetic material.

HyperGen improves genome sketching and ANI estimation by using hyperdimensional vectors, achieving faster performance and lower memory usage than existing methods.

The paper applies molecular clustering to viral genomes to determine pairwise distance thresholds for different viruses, providing guidance for epidemic control.

ViralConsensus efficiently calls viral consensus genomes from read alignments, outperforming existing methods in speed and memory usage.

ViReaDB efficiently stores viral sequence data and computes consensus genomes quickly, reducing storage needs and computational time.

The paper evaluates phylogenetic workflows for viral sequence data, finding that MAFFT is best for alignment, FastTree 2 is fastest for topology, and RAxML-NG optimizes branch lengths efficiently.

SEPIA evaluates prioritization algorithms for HIV transmission risk using simulations, finding ProACT slightly outperforms a distance-based method but both are only marginally better than random.

This paper introduces ProACT, a phylogenetic method for prioritizing HIV-positive individuals based on viral sequence branch lengths to improve public health resource allocation.

CoaTran simulates coalescent viral phylogenies constrained by transmission networks, enabling efficient benchmarking of molecular epidemiology tools.

ViralMSA aligns large viral genome datasets efficiently using a reference-guided approach, scaling linearly with sequence count.

This study analyzes over 4,000 SARS-CoV-2 genomes using ViReport to generate molecular epidemiological reports and track viral evolution.

TreeSwift is a Python package designed to efficiently handle large phylogenetic trees, improving scalability compared to existing tools.

TreeCluster uses phylogenetic trees to cluster biological sequences, improving consistency and downstream application effectiveness.

FAVITES simulates epidemic datasets for fast-evolving pathogens like HIV, enabling study of transmission networks and intervention impacts.

TreeN93 identifies viral transmission clusters without requiring a user-defined distance threshold, using a non-parametric distance-based approach.

The paper introduces a linear-time algorithm for sampling trees under the dual-birth model and provides a C++ implementation.