Daniel E. Cook
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View article: Accurate human genome analysis with element avidity sequencing
Accurate human genome analysis with element avidity sequencing Open
Background New sequencing technologies provide options for the scientific community to design studies and build clinical workflows. These options expand user choice, and can enable more accurate, scalable, or affordable workflows depending…
View article: Pangenome-aware DeepVariant
Pangenome-aware DeepVariant Open
Population-scale genomics information provides valuable prior knowledge for various genomic analyses, especially variant calling. A notable example of such application is the human pangenome reference released by the Human Pangenome Refere…
View article: Clonal driver neoantigen loss under EGFR TKI and immune selection pressures
Clonal driver neoantigen loss under EGFR TKI and immune selection pressures Open
Neoantigen vaccines are under investigation for various cancers, including epidermal growth factor receptor ( EGFR )-driven lung cancers 1,2 . We tracked the phylogenetic history of an EGFR mutant lung cancer treated with erlotinib, osimer…
View article: A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material.
A robust benchmark for detecting low-frequency variants in the HG002 Genome In A Bottle NIST reference material. Open
Somatic mosaicism is an important cause of disease, but mosaic and somatic variants are often challenging to detect because they exist in only a fraction of cells. To address the need for benchmarking subclonal variants in normal cell popu…
View article: Highly accurate assembly polishing with DeepPolisher
Highly accurate assembly polishing with DeepPolisher Open
Accurate genome assemblies are essential for biological research, but even the highest quality assemblies retain errors caused by the technologies used to construct them. Base-level errors are typically fixed with an additional polishing s…
View article: DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies
DeepSomatic: Accurate somatic small variant discovery for multiple sequencing technologies Open
Somatic variant detection is an integral part of cancer genomics analysis. While most methods have focused on short-read sequencing, long-read technologies now offer potential advantages in terms of repeat mapping and variant phasing. We p…
View article: Glial expression of a steroidogenic enzyme underlies natural variation in hitchhiking behavior
Glial expression of a steroidogenic enzyme underlies natural variation in hitchhiking behavior Open
Phoresy is an interspecies interaction that facilitates spatial dispersal by attaching to a more mobile species. Hitchhiking species have evolved specific traits for physical contact and successful phoresy, but the regulatory mechanisms in…
View article: Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads
Severus: accurate detection and characterization of somatic structural variation in tumor genomes using long reads Open
Most current studies rely on short-read sequencing to detect somatic structural variation (SV) in cancer genomes. Long-read sequencing offers the advantage of better mappability and long-range phasing, which results in substantial improvem…
View article: The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes
The Complete Sequence and Comparative Analysis of Ape Sex Chromosomes Open
Apes possess two sex chromosomes—the male-specific Y and the X shared by males and females. The Y chromosome is crucial for male reproduction, with deletions linked to infertility. The X chromosome carries genes vital for reproduction and …
View article: Local read haplotagging enables accurate long-read small variant calling
Local read haplotagging enables accurate long-read small variant calling Open
Long-read sequencing technology has enabled variant detection in difficult-to-map regions of the genome and enabled rapid genetic diagnosis in clinical settings. Rapidly evolving third-generation sequencing platforms like Pacific Bioscienc…
View article: Revolutionizing Inflammatory Bowel Disease Management: A Comprehensive Narrative Review of Innovative Dietary Strategies and Future Directions
Revolutionizing Inflammatory Bowel Disease Management: A Comprehensive Narrative Review of Innovative Dietary Strategies and Future Directions Open
This comprehensive narrative review delves into the intricate interplay between diet and inflammatory bowel disease (IBD), shedding light on the potential impact of dietary interventions in disease management. By analyzing nutritional inte…
View article: Accurate human genome analysis with Element Avidity sequencing
Accurate human genome analysis with Element Avidity sequencing Open
We investigate the new sequencing technology Avidity from Element Biosciences. We show that Element whole genome sequencing achieves higher mapping and variant calling accuracy compared to Illumina sequencing at the same coverage, with lar…
View article: Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome
Pan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome Open
The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. The first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed a k-mer inde…
View article: A Rare but Aggressive Malignancy: A Case Report of a Gastrointestinal Neuroectodermal Tumor (GNET)
A Rare but Aggressive Malignancy: A Case Report of a Gastrointestinal Neuroectodermal Tumor (GNET) Open
Gastrointestinal neuroectodermal tumors (GNETs) are extremely rare and intriguing malignancies originating from neural crest cells in the digestive tract. The digestive tract's neural crest cells can give rise to incredibly unusual and int…
View article: Levofloxacin-Induced Toxic Epidermal Necrolysis
Levofloxacin-Induced Toxic Epidermal Necrolysis Open
Toxic epidermal necrolysis (TEN), also known as Lyell's syndrome, is a severe episodic mucocutaneous reaction that is usually brought on by oral medications and/or sporadically by infections. We report a case of a 19-year-old male with the…
View article: Increased mutation and gene conversion within human segmental duplications
Increased mutation and gene conversion within human segmental duplications Open
Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data 1,2 . Here we constructed 1:1 unambiguous alignments spanning high-ide…
View article: Next generation immuno-oncology tumor profiling using a rapid, non-invasive, computational biophysics biomarker in early-stage breast cancer
Next generation immuno-oncology tumor profiling using a rapid, non-invasive, computational biophysics biomarker in early-stage breast cancer Open
Background Immuno-oncology (IO) therapies targeting the PD-1/PD-L1 axis, such as immune checkpoint inhibitor (ICI) antibodies, have emerged as promising treatments for early-stage breast cancer (ESBC). Despite immunotherapy's clinical sign…