Richard J. Roberts

Genetic engineering of Staphylococcus haemolyticus: Overcoming Restriction-Modification Barriers and Targeting Virulence Genes

This paper develops molecular tools to overcome restriction-modification barriers in Staphylococcus haemolyticus, enabling genome editing and virulence gene targeting.

A virion protein of an archaeal virus inhibits a Type V BREX defense system in Haloarcula hispanica

This study characterizes a Type V BREX defense system in Haloarcula hispanica and shows that two archaeal viruses evade it via a virion protein.

Proxi-RIMS-seq2 applied to native microbiomes uncovers hundreds of known and novel m5C methyltransferase specificities.

The paper applies Proxi-RIMS-seq2 to native microbiomes to identify m5C methylation motifs and their cognate methyltransferases, revealing over 1900 motifs including a novel 8-base recognition site.

Domainator, a flexible software suite for domain-based annotation and neighborhood analysis, identifies proteins involved in antiviral systems

Domainator identifies proteins involved in antiviral systems by clustering and analyzing domain-based gene neighborhoods and integrating a protein language model.

Matching Excellence: ONT's Rise to Parity with PacBio in Genome Reconstruction of Non-Model Bacterium with High GC Content

This study compares ONT and PacBio sequencing for genome reconstruction of high GC content bacteria, finding ONT can achieve high-quality genomes without hybridization.

Rapid Identification of Methylase Specificity (RIMS-seq) jointly identifies methylated motifs and generates shotgun sequencing of bacterial genomes

RIMS-seq identifies methylase specificities and sequences bacterial genomes using a simple protocol, revealing new methylase targets in bacteria and synthetic communities.

Genome-Wide Identification of 5-Methylcytosine Sites in Bacterial Genomes By High-Throughput Sequencing of MspJI Restriction Fragments

The paper introduces MFRE-Seq, a method to identify 5-methylcytosine sites in bacterial genomes using restriction enzyme digestion and sequencing, confirming known motifs and discovering novel ones.

Not All Experimental Questions Are Created Equal: Accelerating Biological Data to Knowledge Transformation (BD2K) via Science Informatics, Active Learning and Artificial Intelligence

The paper proposes a framework to optimize experimental design in biomedical research by prioritizing experiments based on potential information gain using AI and active learning.