Andrew W. Carroll

A complete diploid human genome benchmark for personalized genomics

T2T-HG002v1.1, a complete diploid HG002 assembly lacking detectable errors over 99.4% of its length, enables genome-based benchmarking of assemblies, sequencing reads, and phased variant calls.

A global view of human centromere variation and evolution

The paper assembles and characterizes 2,110 human centromeres, revealing novel haplotypes, mobile element insertions, and mutation rate variation across chromosomes.

Benchmarking long-read variant sensitivity across ONT and PacBio platforms using known clinically reported variants in a cohort of critically ill newborns

Australian giant kelp genome assemblies show distinct Southern Hemisphere genetics

The paper presents two new genome assemblies of Australian giant kelp, showing significant genetic divergence from a Californian reference genome.

PanVariants: Best Practice for Pangenome-based Variant Calling Pipeline and Framework

PanVariants improves variant calling by integrating k-mer and mapping methods, reducing errors and outperforming existing tools for SNVs, indels, and SVs.

A near-complete human pancreatic cancer genome

This paper presents near-complete, haplotype-resolved assemblies of a pancreatic cancer genome and normal tissue, identifying extensive somatic variants and epigenetic changes in previously excluded regions.

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

Pangenome discovery of missing autism variants

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies

DeepSomatic is a deep learning method for detecting somatic variants from short-read and long-read sequencing data, outperforming existing callers, especially for indels.

Rapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe

The paper updates Giraffe to map both long and short reads to large pangenome graphs, showing improved speed and accuracy compared to existing tools.

The Platinum Pedigree: A long-read benchmark for genetic variants

The paper creates a long-read benchmark for genetic variants using a large pedigree, improving variant calling performance and introducing new truth sets for tandem repeats and structural variants.

Accurate human genome analysis with Element Avidity sequencing

This study compares Element Avidity sequencing to Illumina sequencing, finding higher accuracy in mapping and variant calling, especially at lower coverages and in challenging genomic regions.

Highly accurate assembly polishing with DeepPolisher

DeepPolisher improves genome assembly accuracy by reducing errors using a transformer model and phasing method, achieving over 70% indel error reduction.

Pangenome-aware DeepVariant

This paper introduces pangenome-aware DeepVariant, a variant caller that improves accuracy by using a pangenome reference, outperforming linear-reference-based DeepVariant by up to 25.5%.

Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads

Severus detects and characterizes somatic structural variations in tumor genomes using long reads, outperforming existing methods in accuracy and revealing clinically relevant rearrangements.

Small variant benchmark from a complete assembly of X and Y chromosomes

The paper creates a variant benchmark for X and Y chromosomes using a complete assembly of HG002, highlighting challenges in variant detection in complex regions.

A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.

The paper develops a benchmark for detecting low-frequency mosaic variants in the HG002 reference material using high-coverage sequencing data and validates its utility across multiple technologies.

Personalized Pangenome References

The paper introduces a personalized pangenome approach to improve short-read mapping and variant calling by reducing reference bias and errors.

Local read haplotagging enables accurate long-read small variant calling

This paper introduces a local haplotype approximation method to improve variant calling accuracy across long-read sequencing platforms without increasing computational overhead.

Unsupervised representation learning improves genomic discovery and risk prediction for respiratory and circulatory functions and diseases

This paper introduces a deep learning framework, REGLE, that improves genomic discovery and risk prediction for respiratory and circulatory diseases by learning low-dimensional embeddings from high-dimensional clinical data.

The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes

The paper produces gapless assemblies of ape sex chromosomes for five great apes and a lesser ape, revealing divergence in Y chromosomes and evolutionary dynamics.

Utilizing multimodal AI to improve genetic analyses of cardiovascular traits

This paper introduces M-REGLE, a multimodal deep learning method that improves genetic analysis of cardiovascular traits by integrating multiple clinical data modalities and outperforms unimodal approaches in locus discovery and risk prediction.

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

A Draft Human Pangenome Reference

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

Recombination between heterologous human acrocentric chromosomes

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

A Deep-learning based RNA-seq Germline Variant Caller

This paper develops a deep-learning based RNA-seq germline variant caller that outperforms existing tools like Platypus and GATK.

Best: A Tool for Characterizing Sequencing Errors

The paper introduces a tool called best for efficiently quantifying sequencing errors in aligned reads and shows it is 16 times faster than existing methods.

Leveraging deep-learning on raw spirograms to improve genetic understanding and risk scoring of COPD despite noisy labels

This paper trains a deep neural network on noisy COPD labels to predict COPD status from spirograms, improving genetic discovery by identifying new loci and replicating existing ones.

A Complete Pedigree-Based Graph Workflow for Rare Candidate Variant Analysis

The paper introduces a pedigree-aware workflow using pangenome graphs to improve variant calling in rare disease analysis, detecting more deleterious variants in probands than unaffected siblings.

Benchmarking challenging small variants with linked and long reads

This paper expands genome benchmarking to include difficult-to-map regions using linked and long reads, identifying more false negatives in variant calling.