The application of long-read sequencing to cancer

L Ermini, P Driguez - Cancers, 2024 - mdpi.com
Simple Summary Cancer is a complex disease caused by a slew of genetic mutations
discovered through advances in sequencing technologies such as next-generation …

k-mer approaches for biodiversity genomics

KM Jenike, L Campos-Domínguez, M Boddé… - Genome …, 2025 - genome.cshlp.org
The wide array of currently available genomes displays a wonderful diversity in size,
composition, and structure and is quickly expanding thanks to several global biodiversity …

LongTR: genome-wide profiling of genetic variation at tandem repeats from long reads

H Ziaei Jam, JM Zook, S Javadzadeh, J Park, A Sehgal… - Genome Biology, 2024 - Springer
Tandem repeats are frequent across the human genome, and variation in repeat length has
been linked to a variety of traits. Recent improvements in long read sequencing …

Telomere-to-telomere phased genome assembly using HERRO-corrected simplex Nanopore reads

D Stanojević, D Lin, S Nurk, P Florez de Sessions… - bioRxiv, 2024 - biorxiv.org
Telomere-to-telomere phased assemblies have become the norm in genomics. To achieve
these for diploid and even polyploid genomes, the contemporary approach involves a …

Telomere-to-telomere assembly by preserving contained reads

SS Kamath, M Bindra, D Pal, C Jain - Genome Research, 2024 - genome.cshlp.org
Automated telomere-to-telomere (T2T) de novo assembly of diploid and polyploid genomes
remains a formidable task. A string graph is a commonly used assembly graph …

Evaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references

P Sarashetti, J Lipovac, F Tomas, M Šikić, J Liu - Genome biology, 2024 - Springer
Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore
Technologies (ONT) have transformed genomics research by providing diverse data types …

Effects of Food Concentration and Light Intensity on the Growth of a Model Coral

TY Fan, YL Huang, A Mayfield - Oceans, 2024 - mdpi.com
Since reef-building corals rely on both heterotrophy and endosymbiotic dinoflagellate
autotrophy to meet their metabolic needs, it is necessary to consider both food supply and …

Special Issue “Bioinformatics of Unusual DNA and RNA Structures”

M Bartas, V Brázda, P Pečinka - International Journal of Molecular …, 2024 - mdpi.com
Nucleic acids are not only static carriers of genetic information but also play vital roles in
controlling cellular lifecycles through their fascinating structural diversity. Gone are the days …

[HTML][HTML] Cost-Effective Detection of SNPs and Structural Variations in Full-Length Genes of Wheat and Sunflower Using Multiplex PCR and Rapid Nanopore Kit

E Polkhovskaya, E Moskalev, P Merkulov, K Dudnikova… - Biology, 2025 - mdpi.com
The rapid identification of allele variants in target genes is crucial for accelerating marker-
assisted selection (MAS) in plant breeding. Although current high-throughput genoty** …

Measuring DNA contents of animal and plant genomes with Gnodes, the long and short of it

DG Gilbert - bioRxiv, 2024 - biorxiv.org
Measurement of DNA contents of genomes is valuable for understanding genome biology,
including assessments of genome assemblies, but it is not a trivial problem. Measuring …