Andrew B. Stergachis

FiberBrowser converts diverse single-molecule footprinting datasets into a unified representation for analyzing chromatin structure and function across assays.

MaveMD provides a clinical interface for MAVE data to classify variants of uncertain significance and improve genetic medicine outcomes.

The paper analyzes HERV-K(HML-2) structural variation and coding capacity across human pangenomes using long-read sequencing, revealing polymorphic loci and incomplete representation in reference genomes.

The paper shows ecDNA localizes to the nuclear periphery in cancer, resisting silencing and enhancing transcriptional output through interactions with the nuclear lamina.

This study shows that SNAI1 and SNAI2 repressors tune enhancer activity by shifting chromatin states, affecting enhancer function and evolution.

The paper presents an integrated analysis of somatic mosaicism across 25 individuals, revealing tissue-specific mutational processes and epigenetic states.

IsoRanker uses long-read transcriptomics to prioritize non-coding variants in Mendelian conditions by detecting expression outliers, allelic imbalance, and NMD, leading to the identification of pathogenic variants in one individual.

The paper identifies and characterizes human protein-coding duplicated genes using long-read genomic and transcriptomic data, revealing new gene models and constraint patterns.

The paper identifies an essential Ndc10 trimerization interaction in yeast kinetochores that stabilizes centromeric DNA and facilitates kinetochore assembly.

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.

This study benchmarks nine short-read sequencing chemistries across seven sequencers using donor-specific assemblies to measure sequencing errors against sample-matched references, revealing platform-specific error profiles and highlighting the importance of donor-specific references for unbiased comparison.

The paper uses saturation genome editing to assess the functional impact of RAD51D and XRCC2 variants, showing high accuracy in distinguishing pathogenic from benign variants.

This paper introduces MethylSeqNet, a model that improves sequence-based gene regulation predictions by conditioning on CpG methylation, showing benefits for cell-type-specific regulation and allele-specific phenomena.

The paper surveys genetics professionals on their use of functional evidence in variant classification for hearing and vision loss, highlighting challenges in data quality, accessibility, and integration into clinical practice.

The paper recalibrates BAP1 MAVE data for different disease phenotypes to enable accurate variant classification across related disorders.

This study explores patient experiences with genetic variant reclassifications, finding that re-contact practices significantly impact trust and perceived value of genetic testing.

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.

The paper constructs an atlas of telomere variation across humans using long-read sequencing and reveals heritable telomere variant repeats and telomerase-independent extension mechanisms.

The paper develops TRoLR, a pipeline using long-read sequencing to detect and prioritize pathogenic tandem repeat expansions in diverse populations, identifying known and novel expansions with clinical relevance.

MitoScope is a long-read sequencing workflow for mitochondrial genome analysis that improves sensitivity and precision in variant detection and NUMT profiling.

The paper characterizes the genetic diversity and regulatory features of human-specific NOTCH2NL duplications using long-read sequencing and organoid models.

The paper develops a scalable workflow to reclassify variants of uncertain significance using experimental and predictive evidence, resolving 75% of VUS in 40 genes.

This study benchmarks donor-specific assemblies for improved detection of somatic structural variants in a melanoma cell line, finding they identify more variants, especially in repeat-rich regions.

The paper investigates how neocentromeres reshape chromatin and identifies conserved features of native centromeres using haplotype-resolved assemblies and multi-omics data.

This paper introduces DAF-seq, a method for single-molecule and single-cell chromatin fiber sequencing, enabling precise analysis of protein occupancy and chromatin accessibility.

The paper develops iPSC-SGE to assess variant effects in diverse genetic and cell contexts, identifying pathogenic variants and essential disease genes.

This paper optimizes variant prioritization parameters for Exomiser and Genomiser to improve diagnostic yield in rare disease cases using WES and WGS data.

The paper benchmarks somatic variant and indel detection at low allele fractions using short- and long-read data, finding sensitivity and precision around 80% at 300x coverage.

The paper maps somatic mutation burden and functional impact across the cancer genome using telomere-to-telomere sequencing, revealing novel mutation hotspots and regulatory rewiring mechanisms.

The paper uses Fiber-seq to study paternal chromatin repackaging in sperm, finding that protamine lacunae and nucleosome retention play distinct roles in epigenetic inheritance.