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View article: Multimodal epigenetic microarray classifies AML, MDS and controls using peripheral blood
Multimodal epigenetic microarray classifies AML, MDS and controls using peripheral blood Open
Objectives: Aberrant DNA methylation (5mC) and hydroxymethylation (5hmC) patterns are hallmarks of acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS), yet epigenetic markers remain absent from diagnostic workflows. We combine…
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: Enzymatic profiling of cfDNA methylation for detection and monitoring of lung cancer
Enzymatic profiling of cfDNA methylation for detection and monitoring of lung cancer Open
We present a highly sensitive, low-cost approach for detecting lung cancer and monitoring response to therapy, based on sequencing-free detection of methylation biomarkers in cell-free DNA. An engineered methyltransferase is used to fluore…
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: Optical genome and epigenome mapping of clear cell renal cell carcinoma
Optical genome and epigenome mapping of clear cell renal cell carcinoma Open
Cancer cells display complex genomic aberrations that include large-scale genetic rearrangements and epigenetic modulation that are not easily captured by short-read sequencing. This study presents a novel approach for simultaneous profili…
View article: Long-read structural and epigenetic profiling of a kidney tumor-matched sample with nanopore sequencing and optical genome mapping
Long-read structural and epigenetic profiling of a kidney tumor-matched sample with nanopore sequencing and optical genome mapping Open
Carcinogenesis often involves significant alterations in the cancer genome, marked by large structural variants (SVs) and copy number variations (CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogenetic te…
View article: Detection of B Cell Lymphomas By a Simple Epigenetic Blood Test
Detection of B Cell Lymphomas By a Simple Epigenetic Blood Test Open
Background The SANGUINE project is an EU-funded initiative aimed to address the need for minimally invasive, affordable, and accurate molecular testing for the early detection, pathological characterization, and disease monitoring of hemat…
View article: DeepQR: single-molecule QR codes for optical gene-expression analysis
DeepQR: single-molecule QR codes for optical gene-expression analysis Open
Optical imaging and single-molecule imaging, in particular, utilize fluorescent tags in order to differentiate observed species by color. The degree of color multiplexing is dependent on the available spectral detection window and the abil…
View article: Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-Matched Sample with Nanopore Sequencing and Optical Genome Mapping
Long-Read Structural and Epigenetic Profiling of a Kidney Tumor-Matched Sample with Nanopore Sequencing and Optical Genome Mapping Open
Carcinogenesis often involves significant alterations in the cancer genome architecture, marked by large structural and copy number variations (SVs and CNVs) that are difficult to capture with short-read sequencing. Traditionally, cytogene…
View article: Machine-Learning-Based Single-Molecule Quantification of Circulating MicroRNA Mixtures
Machine-Learning-Based Single-Molecule Quantification of Circulating MicroRNA Mixtures Open
MicroRNAs (miRs) are small noncoding RNAs that regulate gene expression and are emerging as powerful indicators of diseases. MiRs are secreted in blood plasma and thus may report on systemic aberrations at an early stage via liquid biopsy …
View article: Single-molecule approaches for DNA damage detection and repair: A focus on Repair Assisted Damage Detection (RADD)
Single-molecule approaches for DNA damage detection and repair: A focus on Repair Assisted Damage Detection (RADD) Open
The human genome is continually exposed to various stressors, which can result in DNA damage, mutations, and diseases. Among the different types of DNA damage, single-strand lesions are commonly induced by external stressors and metabolic …
View article: Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma
Optical Genome and Epigenome Mapping of Clear Cell Renal Cell Carcinoma Open
Cancer cells display complex genomic aberrations that include large-scale genetic rearrangements and epigenetic modulation that are not easily characterized by short-read sequencing. We present a method for simultaneous profiling of long-r…
View article: Genome sequences of three <i>Aegilops</i> species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement
Genome sequences of three <i>Aegilops</i> species of the section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement Open
SUMMARY Aegilops is a close relative of wheat ( Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for the improvement of wheat. To understand their diversity and advance their util…
View article: Genome sequences of<i>Aegilops</i>species of section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement
Genome sequences of<i>Aegilops</i>species of section Sitopsis reveal phylogenetic relationships and provide resources for wheat improvement Open
Aegilops is a close relative of wheat ( Triticum spp.), and Aegilops species in the section Sitopsis represent a rich reservoir of genetic diversity for improvement of wheat. To understand their diversity and advance their utilization, we …
View article: Wild emmer genome architecture and diversity elucidate wheat evolution and domestication
Wild emmer genome architecture and diversity elucidate wheat evolution and domestication Open
Genomics and domestication of wheat Modern wheat, which underlies the diet of many across the globe, has a long history of selection and crosses among different species. Avni et al. used the Hi-C method of genome confirmation capture to as…