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View article: Novel enzymatic DNA produced from a text file achieves comparable immune responses as plasmid vaccine
Novel enzymatic DNA produced from a text file achieves comparable immune responses as plasmid vaccine Open
DNA vaccines have garnered considerable attention due to their recent success in humans for SARS-CoV-2 and immunotherapy for cancer. However, conventional methods for creating and manufacturing DNA vaccines at-scale are slow and rate-limit…
View article: Ultrafast CTCF dynamics control cohesin barrier function
Ultrafast CTCF dynamics control cohesin barrier function Open
CCCTC-binding transcription factor (CTCF) and the cohesin complex shape the genome into loops and topologically associating domains (TADs), yet the mechanisms linking CTCF dynamic behavior to its function as a cohesin barrier remain unclea…
View article: Dynamic changes in mRNA isoform usage during human retinal development
Dynamic changes in mRNA isoform usage during human retinal development Open
Background: Alternative mRNA splicing is a key mechanism for generating isoform diversity in eukaryotic cells. However, the extent of the splicing changes that occur during complex regulatory processes like neurodevelopment are still incom…
View article: Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing
Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing Open
An exciting feature of nanopore sequencing is its ability to record multiomic information on the same sequenced DNA molecule. Well-trained models allow the detection of nucleotide-specific molecular signatures through changes in ionic curr…
View article: Population-scale Long-read Sequencing in the All of Us Research Program
Population-scale Long-read Sequencing in the All of Us Research Program Open
The All of Us Research Program (AoU) is a national biobank seeking to enroll one million individuals in the United States to link genomic and biomedical data, including short- and long-read whole-genome sequencing (srWGS/LRS), with rich el…
View article: A complete diploid human genome benchmark for personalized genomics
A complete diploid human genome benchmark for personalized genomics Open
Human genome resequencing typically involves mapping reads to a reference genome to call variants; however, this approach suffers from both technical and reference biases, leaving many duplicated and structurally polymorphic regions of the…
View article: Single-cell long-read sequencing of the experience-induced transcriptome
Single-cell long-read sequencing of the experience-induced transcriptome Open
Neural activity drives transcriptional events that are critical for learning. Activity-induced transcript isoform expression and alternative splicing are cell-type specific events typically obscured by sequencing approaches that restrict r…
View article: Single-cell RNA sequencing identifies subtypes of cancer-associated fibroblasts in early and late stages of mycosis fungoides
Single-cell RNA sequencing identifies subtypes of cancer-associated fibroblasts in early and late stages of mycosis fungoides Open
Mycosis fungoides (MF), the most common cutaneous T-cell lymphoma, is characterized by infiltration of malignant T-cells into the skin. While early-stage disease (IA-IIA) follows an indolent course, approximately 25% of patients progress t…
View article: Three annotated chromosome-level de novo genome assemblies of <i>Lomentospora prolificans</i> provide evidence for a chromosomal translocation event
Three annotated chromosome-level de novo genome assemblies of <i>Lomentospora prolificans</i> provide evidence for a chromosomal translocation event Open
Lomentospora prolificans is a fungal pathogen responsible for serious, often fatal, illness in patients with compromised immune systems. Treatment is rarely successful because L. prolificans is inherently resistant to all major classes of …
View article: Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing
Write and Read: Harnessing Synthetic DNA Modifications for Nanopore Sequencing Open
An exciting feature of nanopore sequencing is its ability to record multi-omic information on the same sequenced DNA molecule. Well-trained models allow the detection of nucleotide-specific molecular signatures through changes in ionic cur…
View article: Evolution of genome-wide methylation profiling technologies
Evolution of genome-wide methylation profiling technologies Open
In this mini-review, we explore the advancements in genome-wide DNA methylation profiling, tracing the evolution from traditional methods such as methylation arrays and whole-genome bisulfite sequencing to the cutting-edge single-molecule …
View article: Unraveling the hidden complexity of cancer through long-read sequencing
Unraveling the hidden complexity of cancer through long-read sequencing Open
Cancer is fundamentally a disease of the genome, characterized by extensive genomic, transcriptomic, and epigenomic alterations. Most current studies predominantly use short-read sequencing, gene panels, or microarrays to explore these alt…
View article: Evolution and instability of human centromeres are accelerated by heterochromatin boundary loss and CENP-A overexpression
Evolution and instability of human centromeres are accelerated by heterochromatin boundary loss and CENP-A overexpression Open
Summary Centromere location is specified by CENP-A, a centromere-specific histone that epigenetically defines centromere identity. How CENP-A is maintained at one location in rapidly evolving centromeric DNA is unknown. Using single-cell-d…
View article: Three annotated chromosome-level <i>de novo</i> genome assemblies of <i>Lomentospora prolificans</i> provide evidence for a chromosomal translocation event
Three annotated chromosome-level <i>de novo</i> genome assemblies of <i>Lomentospora prolificans</i> provide evidence for a chromosomal translocation event Open
Lomentospora prolificans is a fungal pathogen responsible for serious, often fatal, illness in patients with compromised immune systems. Treatment is rarely successful because L. prolificans is inherently resistant to all major classes of …
View article: Nanopore decoding with speed and versatility for data storage
Nanopore decoding with speed and versatility for data storage Open
Motivation As nanopore technology reaches ever higher throughput and accuracy, it becomes an increasingly viable candidate for reading out DNA data storage. Nanopore sequencing offers considerable flexibility by allowing long reads, real-t…
View article: Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation
Long-read sequencing of hundreds of diverse brains provides insight into the impact of structural variation on gene expression and DNA methylation Open
Structural variants (SVs) drive gene expression in the human brain and are causative of many neurological conditions. However, most existing genetic studies have been based on short-read sequencing methods, which capture fewer than half of…
View article: LARP1 binds ribosomes and TOP mRNAs in repressed complexes
LARP1 binds ribosomes and TOP mRNAs in repressed complexes Open
Terminal oligopyrimidine motif-containing mRNAs (TOPs) encode all ribosomal proteins in mammals and are regulated to tune ribosome synthesis to cell state. Previous studies have implicated LARP1 in 40S- or 80S-ribosome complexes that are t…
View article: Transposon-sequencing (Tn-seq) of the <i>Candida glabrata</i> reference strain CBS138 reveals epigenetic plasticity, structural variation, and intrinsic mechanisms of resistance to micafungin
Transposon-sequencing (Tn-seq) of the <i>Candida glabrata</i> reference strain CBS138 reveals epigenetic plasticity, structural variation, and intrinsic mechanisms of resistance to micafungin Open
Candida glabrata (also called Nakaseomyces glabratus) is an opportunistic pathogen that can resist common antifungals and rapidly acquire multidrug resistance. A large amount of genetic variation exists between isolates, which complicates …
View article: Nanopore Decoding with Speed and Versatility for Data Storage
Nanopore Decoding with Speed and Versatility for Data Storage Open
Motivation As nanopore technology reaches ever higher throughput and accuracy, it becomes an increasingly viable candidate for reading out DNA data storage. Nanopore sequencing offers considerable flexibility by allowing long reads, real-t…
View article: Investigating Subpopulation Dynamics in Clonal CHO-K1 Cells with Single-Cell RNA Sequencing
Investigating Subpopulation Dynamics in Clonal CHO-K1 Cells with Single-Cell RNA Sequencing Open
Chinese Hamster Ovary (CHO) cells are used to produce monoclonal antibodies and other biotherapeutics at industrial scale. Despite their ubiquitous nature in the biopharmaceutical industry, little is known about the behaviors of individual…
View article: Tn-seq of the<i>Candida glabrata</i>reference strain CBS138 reveals epigenetic plasticity, structural variation, and intrinsic mechanisms of resistance to micafungin
Tn-seq of the<i>Candida glabrata</i>reference strain CBS138 reveals epigenetic plasticity, structural variation, and intrinsic mechanisms of resistance to micafungin Open
C. glabrata is an opportunistic pathogen that can resist common antifungals and rapidly acquire multidrug resistance. A large amount of genetic variation exists between isolates, which complicates generalizations. Portable Tn-seq methods c…
View article: Long-Read Nanopore-Based Sequencing of Anelloviruses
Long-Read Nanopore-Based Sequencing of Anelloviruses Open
Routinely used metagenomic next-generation sequencing (mNGS) techniques often fail to detect low-level viremia (<104 copies/mL) and appear biased towards viruses with linear genomes. These limitations hinder the capacity to comprehensively…
View article: Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area
Genomic diversity of SARS-CoV-2 during early introduction into the Baltimore-Washington metropolitan area Open
The early COVID-19 pandemic was characterized by rapid global spread. In Maryland and Washington, DC, United States, more than 2500 cases were reported within 3 weeks of the first COVID-19 detection in March 2020. We aimed to use genomic s…
View article: A genome sequence for the threatened whitebark pine
A genome sequence for the threatened whitebark pine Open
Whitebark pine (WBP, Pinus albicaulis) is a white pine of subalpine regions in the Western contiguous United States and Canada. WBP has become critically threatened throughout a significant part of its natural range due to mortality from t…
View article: Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment
Uncalled4 improves nanopore DNA and RNA modification detection via fast and accurate signal alignment Open
Nanopore signal analysis enables detection of nucleotide modifications from native DNA and RNA sequencing, providing both accurate genetic/transcriptomic and epigenetic information without additional library preparation. Presently, only a …