Julie C. Dunning Hotopp

This study identifies and characterizes long non-coding RNAs in Plasmodium falciparum across asexual and gametocyte stages using long-read sequencing and single-cell transcriptomics.

This study annotates UTRs in Leishmania donovani and finds they vary in length and are enriched in G-quadruplex structures, suggesting a key role in post-transcriptional regulation.

This study investigates rRNA dynamics in Plasmodium falciparum during gametocytogenesis, revealing specific degradation patterns and shifts in rRNA types across developmental stages.

This study finds that laboratory Schistosoma mansoni populations retain abundant genetic variation, with implications for drug resistance studies and GWAS.

The paper predicts bacterial and archaeal transcripts using ONT direct RNA sequencing and public data, revealing novel and previously characterized transcripts across multiple strains.

The paper identifies a false positive in m5C detection by Tombo in GCU motifs across diverse RNA samples, suggesting published findings should be re-evaluated.

This study compares PacBio and Oxford Nanopore long-read sequencing technologies for bacterial and fly genome assembly and methylation detection, finding no single technology outperforms others across all metrics.

The paper compares genome structure, sequence, and immunogenic potential of Plasmodium falciparum strains used in vaccine trials and finds significant differences affecting vaccine efficacy.

This study evaluates the impact of read length and pairing on differential expression analysis in host-pathogen interactions, finding 54-bp paired reads most robust and 36-bp single reads suitable for bacterial samples.

This study compares enrichment techniques for multi-species RNA-Seq, finding that targeted enrichment with Agilent SureSelect improves read mapping to target organisms.

The paper reanalyzes lateral gene transfer (LGT) evidence in vertebrates, concluding that ACY3/ASPA gene distribution likely involves both gene loss and ancient LGT prior to bilaterian divergence.

FADU improves RNA-Seq quantification for prokaryotes by better detecting genes missed by HTSeq and featurecounts, especially in organisms with overlapping transcriptional units and polycistronic transcripts.