Nick Goldman

The paper introduces a new method to discretize Gamma rate distributions in phylogenetics, reducing branch length bias compared to the standard DGM.

The paper identifies BCL11A as a transcription factor that restores differentiation potential in aged oligodendrocyte progenitor cells through computational analysis and experimental validation.

The paper develops PhyCD to detect contamination in SARS-CoV-2 genomes, identifying 10,942 putative contamination events across nearly 5 million genomes.

This paper introduces a site-specific mutation model (SSM) for pandemic-scale phylogenetics, showing it better captures mutation patterns in SARS-CoV-2 genomes than classical models.

CMAPLE 2 improves phylogenetic inference speed and memory efficiency for large pathogen genome datasets, enabling analysis of nearly four million SARS-CoV-2 genomes in 12 days.

The paper improves pandemic-scale phylogenetic analysis by addressing mutation rate variation and sequence errors, reconstructing a reliable phylogenetic tree of over 2 million SARS-CoV-2 genomes.

The paper identifies highly recurrent multi-nucleotide mutations in SARS-CoV-2 and shows they are linked to transcription regulatory sequences, affecting computational evolutionary biology analyses.

This paper introduces a convolutional neural network to detect interspecific positive selection, achieving higher accuracy and robustness to alignment errors compared to traditional statistical methods.

SPRTA assesses phylogenetic confidence by evaluating evolutionary histories rather than clades, applied to a global SARS-CoV-2 dataset.

The paper introduces a hidden Markov model method for protein identification from noisy signature data, showing good performance on a human protein database under various conditions.

This study compares molecular functions and biosynthetic gene clusters in cyanobacterial genomes to identify specializations associated with symbiotic lifestyles.

This study identifies a retroviral origin of vertebrate myelin by showing that RNLTR12-int retrotransposon regulates myelination through SOX10 interaction in multiple vertebrates.

The paper introduces MAPLE, a new phylogenetic analysis method that scales to large datasets by improving computational efficiency, outperforming existing tools like FastTree and RAxML-NG.

This paper introduces BOSS-RUNS, a framework for dynamic nanopore sequencing that adapts in real-time to maximize information gain and reduce coverage bias.

SWAMPy generates realistic SARS-CoV-2 wastewater amplicon metagenomes to test and improve analysis methods.

The paper introduces phastSim, a tool for efficiently simulating sequence evolution on large phylogenetic trees, particularly for SARS-CoV-2-like datasets.

The paper introduces a daily-updated database of SARS-CoV-2 mutation-annotated trees and associated tools for querying and manipulating the data.

The paper introduces phylogenetic novelty scores to weight genetic sequences based on their evolutionary novelty, improving accuracy in character frequency estimation and other applications.

The paper introduces a pair hidden Markov model to detect short-range template switch mutations in great ape genomes and shows their prevalence in evolutionary history.

The paper identifies lab-specific recurrent mutations in SARS-CoV-2 sequences that affect phylogenetic inference and proposes tools to improve sequence quality and phylogeny comparison.

This paper investigates the performance of conditional and unconditional maximum likelihood methods for phylogenetic inference with truncated data and finds they perform similarly in SNP datasets.

PASP measures poly(A) tail lengths across the transcriptome using Illumina sequencing, showing reliable results in yeast with potential for broader application.