Erik Garrison
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View article: Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes
Chromosome-specific epigenetic control and transmission of ribosomal DNA arrays in Hominidae genomes Open
Ribosomal RNA (rRNA) genes are organized in tandem arrays known as ribosomal DNA (rDNA) on multiple chromosomes in Hominidae genomes. We measured copy number and transcriptional activity status of rRNA gene arrays across multiple individua…
View article: The formation and propagation of human Robertsonian chromosomes
The formation and propagation of human Robertsonian chromosomes Open
Robertsonian chromosomes are a type of variant chromosome that is commonly found in nature. Present in 1 in 800 humans, these chromosomes can underlie infertility, trisomies and increased cancer incidence1-5. They have been recognized cyto…
View article: A complete diploid human genome benchmark for personalized genomics
A complete diploid human genome benchmark for personalized genomics Open
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and structurally polymorphic regions of the…
View article: Creating a biomedical knowledge base by addressing GPT inaccurate responses and benchmarking context
Creating a biomedical knowledge base by addressing GPT inaccurate responses and benchmarking context Open
Background We created the GeneNetwork Question Answer system (GNQA), a generative pre-trained transformer (GPT) knowledge base driven by a performant retrieval augmented generation (RAG) with a focus on aging, dementia, Alzheimer’s, and di…
View article: Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocations
Rare k-mers reveal centromere haplogroups underlying human diversity and cancer translocations Open
Centromeres are among the most diverse and dynamically evolving regions of the human genome and are commonly affected in various human cancers. However, organized into highly repetitive α-satellite higher-order repeats (HORs), human centro…
View article: Accurate short-read alignment through<i>r</i>-index-based pangenome indexing
Accurate short-read alignment through<i>r</i>-index-based pangenome indexing Open
Aligning to a linear reference genome can result in a higher percentage of reads going unmapped or being incorrectly mapped owing to variations not captured by the reference, otherwise known as reference bias. Recently, in efforts to mitig…
View article: The mouse pangenome reveals the structural complexity of the murine protein-coding landscape
The mouse pangenome reveals the structural complexity of the murine protein-coding landscape Open
We present the first mouse pangenome consisting of 17 high-quality inbred mouse strain genomes with complete annotation. This collection includes 12 widely used classical laboratory strains and 5 wild-derived strains. We have fully resolve…
View article: <i>wgatools</i>: an ultrafast toolkit for manipulating whole-genome alignments
<i>wgatools</i>: an ultrafast toolkit for manipulating whole-genome alignments Open
Summary With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole-genome alignment…
View article: Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants
Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants Open
Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species…
View article: PanTE: A Comprehensive Framework for Transposable Element Discovery in Graph-based Pangenomes
PanTE: A Comprehensive Framework for Transposable Element Discovery in Graph-based Pangenomes Open
Transposable element (TE) annotation is crucial for understanding genetics, genomics and evolution, yet current methods struggle to identify TEs in graph-based pangenomes. We developed a framework PanTE to construct accurate and representa…
View article: Panacus: fast and exact pangenome growth and core size estimation
Panacus: fast and exact pangenome growth and core size estimation Open
Motivation Using a single linear reference genome poses a limitation to exploring the full genomic diversity of a species. The release of a draft human pangenome underscores the increasing relevance of pangenomics to overcome these limitat…
View article: Creating a Biomedical Knowledge Base by Addressing GPT's Inaccurate Responses and Benchmarking Context
Creating a Biomedical Knowledge Base by Addressing GPT's Inaccurate Responses and Benchmarking Context Open
We created GNQA, a generative pre-trained transformer (GPT) knowledge base driven by a performant retrieval augmented generation (RAG) with a focus on aging, dementia, Alzheimer’s and diabetes. We uploaded a corpus of three thousand peer r…
View article: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
Gapless assembly of complete human and plant chromosomes using only nanopore sequencing Open
The combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human genome and spurred similar efforts to c…
View article: Popping Bubbles in Pangenome Graphs
Popping Bubbles in Pangenome Graphs Open
In this paper, we introduce flubbles, a new definition of "bubbles" corresponding to variants in a (pan)genome graph $G$. We then show a characterization for flubbles in terms of equivalence classes regarding cycles in an intermediate data…
View article: Creating a biomedical knowledge base by addressing GPT inaccurate responses and benchmarking context
Creating a biomedical knowledge base by addressing GPT inaccurate responses and benchmarking context Open
We created GNQA, a generative pre-trained transformer (GPT) knowledge base driven by a performant retrieval augmented generation (RAG) with a focus on aging, dementia, Alzheimer’s and diabetes. We uploaded a corpus of three thousand peer r…
View article: Efficient indexing and querying of annotations in a pangenome graph
Efficient indexing and querying of annotations in a pangenome graph Open
The current reference genome is the backbone of diverse and rich annotations. Simple text formats, like VCF or BED, have been widely adopted and helped the critical exchange of genomic information. There is a dire need for tools and format…
View article: Cluster-efficient pangenome graph construction with nf-core/pangenome
Cluster-efficient pangenome graph construction with nf-core/pangenome Open
Motivation Pangenome graphs offer a comprehensive way of capturing genomic variability across multiple genomes. However, current construction methods often introduce biases, excluding complex sequences or relying on references. The PanGeno…
View article: The Platinum Pedigree: A long-read benchmark for genetic variants
The Platinum Pedigree: A long-read benchmark for genetic variants Open
Recent advances in genome sequencing have improved variant calling in complex regions of the human genome. However, it is difficult to quantify variant calling performance since existing standards often focus on specificity, neglecting com…
View article: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation Open
Fewer than half of individuals with a suspected Mendelian or monogenic condition receive a precise molecular diagnosis after comprehensive clinical genetic testing. Improvements in data quality and costs have heightened interest in using l…
View article: The formation and propagation of human Robertsonian chromosomes
The formation and propagation of human Robertsonian chromosomes Open
Robertsonian chromosomes are a type of variant chromosome found commonly in nature. Present in one in 800 humans, these chromosomes can underlie infertility, trisomies, and increased cancer incidence. Recognized cytogenetically for more th…
View article: Pangenome-Informed Language Models for Synthetic Genome Sequence Generation
Pangenome-Informed Language Models for Synthetic Genome Sequence Generation Open
Language Models (LM) have been extensively utilized for learning DNA sequence patterns and generating synthetic sequences. In this paper, we present a novel approach for the generation of synthetic DNA data using pangenomes in combination …
View article: Epigenetic control and inheritance of rDNA arrays
Epigenetic control and inheritance of rDNA arrays Open
Ribosomal RNA (rRNA) genes exist in multiple copies arranged in tandem arrays known as ribosomal DNA (rDNA). The total number of gene copies is variable, and the mechanisms buffering this copy number variation remain unresolved. We surveye…
View article: Recurrent evolution and selection shape structural diversity at the amylase locus
Recurrent evolution and selection shape structural diversity at the amylase locus Open
The adoption of agriculture triggered a rapid shift towards starch-rich diets in human populations 1 . Amylase genes facilitate starch digestion, and increased amylase copy number has been observed in some modern human populations with hig…
View article: Rapid GPU-Based Pangenome Graph Layout
Rapid GPU-Based Pangenome Graph Layout Open
Computational Pangenomics is an emerging field that studies genetic variation using a graph structure encompassing multiple genomes. Visualizing pangenome graphs is vital for understanding genome diversity. Yet, handling large graphs can b…
View article: A familial, telomere-to-telomere reference for human<i>de novo</i>mutation and recombination from a four-generation pedigree
A familial, telomere-to-telomere reference for human<i>de novo</i>mutation and recombination from a four-generation pedigree Open
Using five complementary short- and long-read sequencing technologies, we phased and assembled >95% of each diploid human genome in a four-generation, 28-member family (CEPH 1463) allowing us to systematically assess de novo mutations (DNM…
View article: Pangenome graph layout by Path-Guided Stochastic Gradient Descent
Pangenome graph layout by Path-Guided Stochastic Gradient Descent Open
Motivation The increasing availability of complete genomes demands for models to study genomic variability within entire populations. Pangenome graphs capture the full genomic similarity and diversity between multiple genomes. In order to …