Conrad A. Nieduszynski

Single-molecule landscape of DNA replication pausing

The paper identifies replication pause sites in a eukaryotic genome using long-read nanopore sequencing and finds they are enriched near transcribed regions and correlate with transcription and R-loop levels.

Single-molecule sequencing maps replication dynamics across the fission yeast genome, including centromeres

This paper introduces DNAscent, a nanopore sequencing method to map DNA replication dynamics in fission yeast at single-molecule resolution, revealing replication patterns in centromeres and rDNA.

Most human DNA replication initiation is dispersed throughout the genome with only a minority within previously identified initiation zones

The paper uses single-molecule sequencing to show most DNA replication initiation in human cells occurs at dispersed sites, not just previously identified zones.

Telomere-to-telomere Schizosaccharomyces japonicus genome assembly reveals hitherto unknown genome features

The paper presents a telomere-to-telomere genome assembly of S. japonicus, revealing a previously unknown second centromere-like region and revising the genome size estimate.

Design, Construction, and Functional Characterization of a tRNA Neochromosome in Yeast

A de novo yeast neochromosome carrying all 275 tRNA genes was built and characterized; it imposes a growth burden, with genome doubling and deletions in haploids possibly reflecting compensation.

Resistance to miltefosine results from amplification of the RTA3 floppase or inactivation of flippases in Candida parapsilosis

This study identifies that resistance to miltefosine in Candida parapsilosis arises from RTA3 gene amplification or flippase inactivation, altering plasma membrane lipid asymmetry.

Sir2 mitigates an intrinsic imbalance in origin licensing efficiency between early and late replicating euchromatin

The paper shows Sir2 regulates MCM complex distribution in yeast chromosomes to ensure proper origin licensing and genome duplication.

The Beacon Calculus: A formal method for the flexible and concise modelling of biological systems

The paper introduces the Beacon Calculus, a process algebra for modelling biological systems, and demonstrates its application to DNA replication, DNA damage repair, and multisite phosphorylation.

Inter-species conservation of organisation and function between non-homologous regional centromeres

The paper shows that centromere DNA from non-homologous fission yeast species can be recognized and function across species, despite lacking sequence conservation.

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

This paper introduces a method to measure DNA replication dynamics on single molecules using nanopore sequencing and applies it to yeast to discover new replication origins.

Cohesin-mediated genome architecture does not define DNA replication timing domains

This study shows that cohesin-mediated genome architecture is not required for replication timing patterns during S phase or G1.

Modeling of DNA replication in rapidly growing bacteria with one and two replication origins

The paper models DNA replication in bacteria with one and two origins, predicting replication profile gradients and altered parameters in double origin strains.

Rapid high-resolution measurement of DNA replication timing by droplet digital PCR

This paper introduces a droplet digital PCR method for high-resolution DNA replication timing measurement, showing it is faster and more cost-effective than sequencing-based approaches while maintaining comparable resolution.