Jeffrey Rosenfeld

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.

The complete sequence of a human genome

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

A complete reference genome improves analysis of human genetic variation

The T2T-CHM13 reference genome improves read mapping and variant calling across diverse samples, reducing false positives and enabling novel variant discovery.

Shotgun Transcriptome and Isothermal Profiling of SARS-CoV-2 Infection Reveals Unique Host Responses, Viral Diversification, and Drug Interactions

This study uses rapid diagnostics and metatranscriptomics to analyze SARS-CoV-2 infection, revealing viral evolution, host responses, and drug interactions in NYC samples.

Whole Genome Sequencing and Assembly of the Asian Honey Bee Apis dorsata

This study sequenced and assembled the genome of the Asian honey bee Apis dorsata, identifying unique genes and transposable elements associated with its defensive behavior.

A robust benchmark for germline structural variant detection

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

Single-Cell, Human Sperm Transcriptomes and Variants from Fathers of Autistic and Healthy Children

The paper analyzes single-cell sperm RNA-seq data from fathers of autistic and healthy children to identify mutation clusters and expression differences associated with ASD risk.