Bryan Thornlow
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View article: Pan-cancer multi-omic model of LINE-1 activity reveals locus heterogeneity of retrotransposition efficiency
Pan-cancer multi-omic model of LINE-1 activity reveals locus heterogeneity of retrotransposition efficiency Open
Somatic mobilization of LINE-1 (L1) has been implicated in cancer etiology. We analyzed a recent TCGA data release comprised of nearly 5000 pan-cancer paired tumor-normal whole-genome sequencing (WGS) samples and ~9000 tumor RNA samples. W…
View article: DecentTree: scalable Neighbour-Joining for the genomic era
DecentTree: scalable Neighbour-Joining for the genomic era Open
Motivation Neighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10 000 sequences. Given the increasing pace of genera…
View article: Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than <i>de novo</i> and Maximum-Likelihood Implementations
Online Phylogenetics with matOptimize Produces Equivalent Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than <i>de novo</i> and Maximum-Likelihood Implementations Open
Phylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have …
View article: Transposable elements drive intron gain in diverse eukaryotes
Transposable elements drive intron gain in diverse eukaryotes Open
There is massive variation in intron numbers across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive. Rapid intron loss and gain in some lineages contrast with long-term evolutionary stasis in oth…
View article: matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2
matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2 Open
This is the 100K-sample tree and 1M-sample tree used for benchmarking matOptimize and TNT.
View article: matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2
matOptimize: a parallel tree optimization method enables online phylogenetics for SARS-CoV-2 Open
Motivation Phylogenetic tree optimization is necessary for precise analysis of evolutionary and transmission dynamics, but existing tools are inadequate for handling the scale and pace of data produced during the coronavirus disease 2019 (…
View article: Supplement to Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination
Supplement to Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination Open
Extended Data S1-S2 and Tables S6-S9 corresponding to the publication entitled Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination. Data S1 contains the phylogeny analyzed in the aforementioned study, and Data S2 co…
View article: Supplement to Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination
Supplement to Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination Open
Extended Data S1-S2 and Tables S6-S9 corresponding to the publication entitled Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination. Data S1 contains the phylogeny analyzed in the aforementioned study, and Data S2 co…
View article: Supplement to Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination
Supplement to Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination Open
Extended Data S1-S2 and Tables S6-S9 corresponding to the publication entitled Pandemic-Scale Phylogenomics Reveals A Landscape of SARS-CoV2 Recombination. Data S1 contains the phylogeny analyzed in the aforementioned study, and Data S2 co…
View article: Transposable elements drive intron gain in diverse eukaryotes
Transposable elements drive intron gain in diverse eukaryotes Open
There is massive variation in intron numbers across eukaryotic genomes, yet the major drivers of intron content during evolution remain elusive. Rapid intron loss and gain in some lineages contrasts with long term evolutionary stasis in ot…
View article: DecentTree: Scalable Neighbour-Joining for the Genomic Era
DecentTree: Scalable Neighbour-Joining for the Genomic Era Open
Summary Neighbour-Joining is one of the most widely used distance-based phylogenetic inference methods. However, current implementations do not scale well for datasets with more than 10,000 sequences. Given the increasing pace of generatin…
View article: Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures
Eukaryotic tRNA sequences present conserved and amino acid-specific structural signatures Open
Metazoan organisms have many tRNA genes responsible for decoding amino acids. The set of all tRNA genes can be grouped in sets of common amino acids and isoacceptor tRNAs that are aminoacylated by corresponding aminoacyl-tRNA synthetases. …
View article: matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2
matOptimize: A parallel tree optimization method enables online phylogenetics for SARS-CoV-2 Open
Phylogenetic tree optimization is necessary for precise analysis of evolutionary and transmission dynamics, but existing tools are inadequate for handling the scale and pace of data produced during the COVID-19 pandemic. One transformative…
View article: Mt_africanum_GCF_000195955.2.final.vcf.genozip
Mt_africanum_GCF_000195955.2.final.vcf.genozip Open
Multisample VCF consisting of 10,248 Mycobacterium tuberculosis samples. Compressed with genozip (https://genozip.readthedocs.io/)
View article: Pandemic-scale phylogenetics
Pandemic-scale phylogenetics Open
1. Abstract Phylogenetics has been central to the genomic surveillance, epidemiology and contact tracing efforts during the COVD-19 pandemic. But the massive scale of genomic sequencing has rendered the pre-pandemic tools inadequate for co…
View article: Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than <i>de novo</i> and Maximum-Likelihood Approaches
Online Phylogenetics using Parsimony Produces Slightly Better Trees and is Dramatically More Efficient for Large SARS-CoV-2 Phylogenies than <i>de novo</i> and Maximum-Likelihood Approaches Open
Phylogenetics has been foundational to SARS-CoV-2 research and public health policy, assisting in genomic surveillance, contact tracing, and assessing emergence and spread of new variants. However, phylogenetic analyses of SARS-CoV-2 have …
View article: A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees
A Daily-Updated Database and Tools for Comprehensive SARS-CoV-2 Mutation-Annotated Trees Open
The vast scale of SARS-CoV-2 sequencing data has made it increasingly challenging to comprehensively analyze all available data using existing tools and file formats. To address this, we present a database of SARS-CoV-2 phylogenetic trees …
View article: Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region
Pandemic-Scale Phylogenomics Reveals Elevated Recombination Rates in the SARS-CoV-2 Spike Region Open
Accurate and timely detection of recombinant lineages is crucial for interpreting genetic variation, reconstructing epidemic spread, identifying selection and variants of interest, and accurately performing phylogenetic analyses. During th…
View article: A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control
A new SARS-CoV-2 lineage that shares mutations with known Variants of Concern is rejected by automated sequence repository quality control Open
We report a SARS-CoV-2 lineage that shares N501Y, P681H, and other mutations with known variants of concern, such as B.1.1.7. This lineage, which we refer to as B.1.x (COG-UK sometimes references similar samples as B.1.324.1), is present i…
View article: A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees
A daily-updated database and tools for comprehensive SARS-CoV-2 mutation-annotated trees Open
The vast scale of SARS-CoV-2 sequencing data has made it increasingly challenging to comprehensively analyze all available data using existing tools and file formats. To address this, we present a database of SARS-CoV-2 phylogenetic trees …
View article: Stability of SARS-CoV-2 phylogenies
Stability of SARS-CoV-2 phylogenies Open
The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and…
View article: Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic
Ultrafast Sample Placement on Existing Trees (UShER) Empowers Real-Time Phylogenetics for the SARS-CoV-2 Pandemic Open
As the SARS-CoV-2 virus spreads through human populations, the unprecedented accumulation of viral genome sequences is ushering a new era of “genomic contact tracing” – that is, using viral genome sequences to trace local transmission dyna…
View article: Stability of SARS-CoV-2 Phylogenies
Stability of SARS-CoV-2 Phylogenies Open
The SARS-CoV-2 pandemic has led to unprecedented, nearly real-time genetic tracing due to the rapid community sequencing response. Researchers immediately leveraged these data to infer the evolutionary relationships among viral samples and…
View article: Predicting transfer RNA gene activity from sequence and genome context
Predicting transfer RNA gene activity from sequence and genome context Open
Transfer RNA (tRNA) genes are among the most highly transcribed genes in the genome owing to their central role in protein synthesis. However, there is evidence for a broad range of gene expression across tRNA loci. This complexity, combin…
View article: Predicting transfer RNA gene activity from sequence and genome context
Predicting transfer RNA gene activity from sequence and genome context Open
Transfer RNA (tRNA) genes are among the most highly transcribed genes in the genome due to their central role in protein synthesis. However, there is evidence for a broad range of gene expression across tRNA loci. This complexity, combined…
View article: Estimating the Timing of Multiple Admixture Pulses During Local Ancestry Inference
Estimating the Timing of Multiple Admixture Pulses During Local Ancestry Inference Open
Admixture, the mixing of genetically distinct populations, is increasingly recognized as a fundamental biological process. One major goal of admixture analyses is to estimate the timing of admixture events. Whereas most methods today can o…
View article: Transfer RNA genes experience exceptionally elevated mutation rates
Transfer RNA genes experience exceptionally elevated mutation rates Open
Significance While transcription-associated mutagenesis (TAM) has been demonstrated for protein-coding genes, its implications in shaping genome structure at transfer RNA (tRNA) loci in metazoans have not been fully appreciated. We show th…