Bryce Kille
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View article: Seqwin: Ultrafast identification of signature sequences in microbial genomes
Seqwin: Ultrafast identification of signature sequences in microbial genomes Open
Motivation Polymerase chain reaction (PCR) enables rapid, cost-effective diagnostics but requires prior identification of genomic regions that allow sensitive and specific identification of target microbial groups, herein referred to as mi…
View article: Complete sequencing of ape genomes
Complete sequencing of ape genomes Open
The most dynamic and repetitive regions of great ape genomes have traditionally been excluded from comparative studies 1–3 . Consequently, our understanding of the evolution of our species is incomplete. Here we present haplotype-resolved …
View article: tMHG-Finder: Tree-guided Maximal Homologous Group Finder for Bacterial Genomes
tMHG-Finder: Tree-guided Maximal Homologous Group Finder for Bacterial Genomes Open
A maximal homologous group , or MHG, as a group of sequences with a shared evolutionary ancestry, shifts the focus from a genecentric view to a homology-centric view in comparative genomic studies. Each MHG is formed by identifying and gro…
View article: A near-tight lower bound on the density of forward sampling schemes
A near-tight lower bound on the density of forward sampling schemes Open
Motivation Sampling k-mers is a ubiquitous task in sequence analysis algorithms. Sampling schemes such as the often-used random minimizer scheme are particularly appealing as they guarantee at least one k-mer is selected out of every w con…
View article: A near-tight lower bound on the density of forward sampling schemes
A near-tight lower bound on the density of forward sampling schemes Open
Motivation Sampling k -mers is a ubiquitous task in sequence analysis algorithms. Sampling schemes such as the often-used random minimizer scheme are particularly appealing as they guarantee at least one k -mer is selected out of every w c…
View article: Complete sequencing of ape genomes
Complete sequencing of ape genomes Open
We present haplotype-resolved reference genomes and comparative analyses of six ape species, namely: chimpanzee, bonobo, gorilla, Bornean orangutan, Sumatran orangutan, and siamang. We achieve chromosome-level contiguity with unparalleled …
View article: Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
Olivar: towards automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens Open
Tiled amplicon sequencing has served as an essential tool for tracking the spread and evolution of pathogens. Over 15 million complete SARS-CoV-2 genomes are now publicly available, most sequenced and assembled via tiled amplicon sequencin…
View article: Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet
Lightweight taxonomic profiling of long-read metagenomic datasets with Lemur and Magnet Open
The advent of long-read sequencing of microbiomes necessitates the development of new taxonomic profilers tailored to long-read shotgun metagenomic datasets. Here, we introduce Lemur and Magnet, a pair of tools optimized for lightweight an…
View article: Parsnp 2.0: scalable core-genome alignment for massive microbial datasets
Parsnp 2.0: scalable core-genome alignment for massive microbial datasets Open
Motivation Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, the process of identifying nucleotides across multiple genomes which share a common ancestor,…
View article: Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets
Parsnp 2.0: Scalable Core-Genome Alignment for Massive Microbial Datasets Open
Motivation Since 2016, the number of microbial species with available reference genomes in NCBI has more than tripled. Multiple genome alignment, the process of identifying nucleotides across multiple genomes which share a common ancestor,…
View article: Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation
Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation Open
Motivation The Jaccard similarity on k-mer sets has shown to be a convenient proxy for sequence identity. By avoiding expensive base-level alignments and comparing reduced sequence representations, tools such as MashMap can scale to massiv…
View article: Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation
Minmers are a generalization of minimizers that enable unbiased local Jaccard estimation Open
1 Abstracts Motivation The Jaccard similarity on k -mer sets has shown to be a convenient proxy for sequence identity. By avoiding expensive base-level alignments and comparing reduced sequence representations, tools such as MashMap can sc…
View article: Ultra-high throughput mapping of genetic design space
Ultra-high throughput mapping of genetic design space Open
Massively parallel genetic screens have been used to map sequence-to-function relationships for a variety of genetic elements. However, because these approaches only interrogate short sequences, it remains challenging to perform high throu…
View article: Catalytic Site Proximity Profiling for Functional Unification of Sequence-Diverse Radical <i>S</i>-Adenosylmethionine Enzymes
Catalytic Site Proximity Profiling for Functional Unification of Sequence-Diverse Radical <i>S</i>-Adenosylmethionine Enzymes Open
The radical S-adenosylmethionine (rSAM) superfamily has become a wellspring for discovering new enzyme chemistry, especially regarding ribosomally synthesized and post-translationally modified peptides (RiPPs). Here, we report a compendium…
View article: Olivar: automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens
Olivar: automated variant aware primer design for multiplex tiled amplicon sequencing of pathogens Open
Tiled amplicon sequencing has served as an essential tool for tracking the spread and evolution of pathogens. Over 2 million complete SARS-CoV-2 genomes are now publicly available, most sequenced and assembled via tiled amplicon sequencing…
View article: Peptidase Activation by a Leader Peptide-Bound RiPP Recognition Element
Peptidase Activation by a Leader Peptide-Bound RiPP Recognition Element Open
The RiPP precursor recognition element (RRE) is a conserved domain found in many prokaryotic ribosomally synthesized and post-translationally modified peptide (RiPP) biosynthetic gene clusters (BGCs). RREs bind with high specificity and af…
View article: Efficient Reconciliation of Genomic Datasets of High Similarity
Efficient Reconciliation of Genomic Datasets of High Similarity Open
We apply Invertible Bloom Lookup Tables (IBLTs) to the comparison of k-mer sets originated from large DNA sequence datasets. We show that for similar datasets, IBLTs provide a more space-efficient and, at the same time, more accurate metho…
View article: Bioinformatics-Guided Expansion and Discovery of Graspetides
Bioinformatics-Guided Expansion and Discovery of Graspetides Open
Graspetides are a class of ribosomally synthesized and post-translationally modified peptide natural products featuring ATP-grasp ligase-dependent formation of macrolactones/macrolactams. These modifications arise from serine, threonine, o…
View article: Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data
Rescuing Low Frequency Variants within Intra-Host Viral Populations directly from Oxford Nanopore sequencing data Open
Infectious disease monitoring on Oxford Nanopore Technologies (ONT) platforms offers rapid turnaround times and low cost, exemplified by well over a half of million ONT SARS-COV-2 datasets. Tracking low frequency intra-host variants has pr…
View article: An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates Open
In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related rese…
View article: Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets
Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets Open
With recent advances in sequencing technology it has become affordable and practical to sequence genomes to very high depth-of-coverage, allowing researchers to discover low-frequency variants in the genome. However, due to the errors in s…
View article: Accelerating SARS-CoV-2 low frequency variant calling on ultra deep\n sequencing datasets
Accelerating SARS-CoV-2 low frequency variant calling on ultra deep\n sequencing datasets Open
With recent advances in sequencing technology it has become affordable and\npractical to sequence genomes to very high depth-of-coverage, allowing\nresearchers to discover low-frequency variants in the genome. However, due to\nthe errors i…
View article: Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets
Accelerating SARS-CoV-2 low frequency variant calling on ultra deep sequencing datasets Open
With recent advances in sequencing technology it has become affordable and practical to sequence genomes to very high depth-of-coverage, allowing researchers to discover low-frequency variants in the genome. However, due to the errors in s…
View article: SeqScreen: Accurate and Sensitive Functional Screening of Pathogenic Sequences via Ensemble Learning
SeqScreen: Accurate and Sensitive Functional Screening of Pathogenic Sequences via Ensemble Learning Open
The COVID-19 pandemic has emphasized the importance of detecting known and emerging pathogens from clinical and environmental samples. However, robust characterization of pathogenic sequences remains an open challenge. To this end, we deve…
View article: An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates
An international virtual hackathon to build tools for the analysis of structural variants within species ranging from coronaviruses to vertebrates Open
In October 2020, 62 scientists from nine nations worked together remotely in the Second Baylor College of Medicine & DNAnexus hackathon, focusing on different related topics on Structural Variation, Pan-genomes, and SARS-CoV-2 related rese…