Zev N. Kronenberg

Isocall enables scalable transcript identification from long-read RNA-sequencing data

Isocall is a scalable method for joint transcript identification from long-read RNA-seq data, showing high precision and handling large datasets efficiently.

Hunting for microsatellite instability in long-read data with Owl

Owl quantifies microsatellite instability from long-read data, identifying MSI-high genomes and motif-specific patterns in cancer samples.

Aardvark: Sifting through differences in a mound of variants

Aardvark benchmarks genomic variant calling accuracy by comparing haplotype sequences with a basepair score, supporting multiple variant types and outperforming hap.py.

A family portrait of the genomic factors shaping tandem repeat mutagenesis

This study identifies genomic factors influencing tandem repeat mutagenesis using long-read sequencing in a large family, finding that de novo mutations are more common at longer, uninterrupted, and heterozygous loci.

Resolution of the D4Z4 repeat responsible for facioscapulohumeral muscular dystrophy with HiFi sequencing

The paper introduces Kivvi, a tool to genotype D4Z4 repeats using HiFi sequencing, enabling accurate detection of FSHD-related alleles and revealing genetic diversity across populations.

A computational model for quantifying instability of tandem repeats across the genome

The paper introduces a computational model to quantify tandem repeat instability using long-read sequencing data and applies it to identify unstable alleles in 256 HPRC cell lines.

Population-scale interpretation of RNA isoform diversity enabled by Isopedia

Isopedia reduces apparent isoform novelty by up to 26-fold in HG002 benchmarks and provides a reference-agnostic framework for population-scale isoform annotation.

Portello: Making global assembly more effective for rare-disease whole genome sequencing

Portello improves variant calling accuracy in rare-disease whole genome sequencing by aligning de novo assembly contigs to a reference genome, reducing basecall errors and enabling better interpretation of complex loci.

Complex structural variant visualization with SVTopo

SVTopo visualizes complex structural variants using high-accuracy long reads, providing clear figures to understand multi-breakpoint events in human genomes.

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.

Multimodal single-cell analyses reveal distinct fusion-regulated transcriptional programs in Ewing sarcoma.

The paper identifies distinct transcriptional programs in Ewing sarcoma driven by EWS::FLI1 fusions and shows their variability across tumors and cell lines.

A familial, telomere-to-telomere reference for human de novo mutation and recombination from a four-generation pedigree

The paper uses a four-generation family to systematically assess de novo mutations and recombination, finding high mutation rates and paternal bias, along with a detailed recombination map.

Sawfish: Improving long-read structural variant discovery and genotyping with local haplotype modeling

Sawfish improves long-read structural variant calling accuracy by modeling local haplotypes, outperforming existing tools in benchmark tests and joint-genotyping analyses.

StarPhase: Comprehensive Phase-Aware Pharmacogenomic Diplotyper for Long-Read Sequencing Data

StarPhase diplotypes 21 pharmacogenes using long-read sequencing with high accuracy, updating 26.2% of existing diplotypes and highlighting gaps in pharmacogenomic databases.

TRGT-denovo: accurate detection of de novo tandem repeat mutations

TRGT-denovo accurately detects de novo tandem repeat mutations in family trios, reducing false positives and improving precision compared to genotype-based methods.

Closing the gap: Solving complex medically relevant genes at scale

The paper introduces a targeted sequencing framework, TADGP, that accurately calls variants in complex medically relevant genes at lower cost than HiFi-WGS, enabling scalable analysis of dark genomic regions.

Assembly and annotation of two high-quality columbid reference genomes from sequencing of a Columba livia x Columba guinea F1 hybrid

The paper presents high-quality genome assemblies and annotations for two pigeon species using long-read sequencing of an F1 hybrid, improving genomic resources for comparative genomics and functional studies.

Resolving the unsolved: Comprehensive assessment of tandem repeats at scale

The paper introduces TRGT, a tool for tandem repeat genotyping, and a database of 937,122 TRs across 100 genomes, achieving high concordance and detecting repeat expansions, methylation, and mosaicism.

HiPhase: Jointly phasing small and structural variants from HiFi sequencing

HiPhase jointly phases small and structural variants from HiFi sequencing, achieving improved phase block NG50 and gene phasing rates.

Deep haplotype analyses of target-site resistance locus ACCase in blackgrass enabled by pool-based amplicon sequencing

The paper uses pool-based amplicon sequencing to analyze haplotype diversity at the ACCase resistance locus in blackgrass, revealing common soft sweeps and the persistence of TSR haplotypes.

Vcflib and tools for processing the VCF variant call format

A C++ library plus 83 command line utilities and 44 scripts (vcflib) for filtering, transforming and computing population-genetic statistics on VCF files, with companion tools bio-vcf, slivar, cyvcf2 and hts-nim.

Towards complete and error-free genome assemblies of all vertebrate species

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

Extended haplotype phasing of de novo genome assemblies with FALCON-Phase

FALCON-Phase uses long-read sequencing and Hi-C data to create phased diploid genome assemblies, achieving high accuracy in non-human species but lower accuracy in humans.

A copy number variant is associated with a spectrum of pigmentation patterns in the rock pigeon (Columba livia)

The paper identifies a copy number variant at the St locus associated with pigmentation patterns in rock pigeons, linking structural variation to gene expression and phenotypic diversity.

Improved assembly and variant detection of a haploid human genome using single-molecule, high-fidelity long reads

This study compares HiFi and CLR long-read sequencing for human genome assembly, finding HiFi provides better continuity and accuracy in complex regions but not centromeres or segmental duplications.

Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants

The paper presents a high-quality long-read genome assembly of the Chinese rhesus macaque and identifies ape-specific structural variants.

Haplotype-Resolved Cattle Genomes Provide Insights Into Structural Variation and Adaptation

The paper presents haplotype-resolved cattle genomes to identify structural variants and adaptation traits, finding expanded immune-related gene families and a fatty acid desaturase copy under positive selection in indicine cattle.

Multi-platform discovery of haplotype-resolved structural variation in human genomes

This study identifies a large number of structural variants in human genomes using multiple sequencing technologies and presents them as a gold standard for future studies.

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

The paper uses chimpanzee cerebral organoids to identify human-specific genes in cortical development and finds increased PI3K/AKT/mTOR activation in human outer radial glia.

Comparative Annotation Toolkit (CAT) - simultaneous clade and personal genome annotation

The paper introduces CAT, a toolkit for simultaneous clade and personal genome annotation, demonstrating its ability to discover novel genes and improve cross-species RNA expression analysis.