Rodrigo P. Baptista

Optimizing genome assembly, chromosome synteny, and genetic variant discovery from Oxford Nanopore sequences of Dermacentor reticulatus ticks

The paper optimizes genome assembly and variant discovery for Dermacentor reticulatus ticks using Oxford Nanopore sequencing, identifying workflow parameters that yield high-quality assemblies and genetic insights.

Genome-targeted enrichment and sequencing of human-infecting Cryptosporidium spp.

The paper develops and validates a set of 100,000 RNA baits (CryptoCap_100k) to enrich Cryptosporidium DNA from clinical and environmental samples, improving read mapping, coverage, and variant analysis while reducing costs.

Loss of the Ferripyochelin Receptor FptA Drives Reduced Cefiderocol Susceptibility and Impairs Fitness in Pseudomonas aeruginosa PA14

This study identifies FptA inactivation as a key step in cefiderocol resistance in Pseudomonas aeruginosa PA14, revealing resistance mechanisms and fitness costs.

Deciphering Transcription in Cryptosporidium parvum: Polycistronic Gene Expression and Chromatin Accessibility

This study identifies polycistronic mRNA expression in Cryptosporidium parvum using long-read RNA-seq and ATAC-seq, revealing a novel gene regulation mechanism in apicomplexan parasites.

A new chromosome-level genome assembly and annotation of Cryptosporidium meleagridis

The paper presents a chromosome-level genome assembly and annotation of Cryptosporidium meleagridis, revealing 3,923 protein-coding genes and high completeness.

The repetitive genome of the Ixodes ricinus tick reveals transposable elements have driven genome evolution in ticks

The paper generates high-quality genome assemblies for Ixodes ricinus and identifies transposable elements as major drivers of genome evolution in ticks.

Evaluating the Benefits and Limits of Multiple Displacement Amplification with Whole-Genome Oxford Nanopore Sequencing

This study evaluates MDA's effectiveness for genome assembly with ONT sequencing, showing high-quality results from low DNA input and introducing a tool to mitigate concatemeric sequences.

New T2T assembly of Cryptosporidium parvum IOWA annotated with reference genome gene identifiers

The paper presents a gapless telomere-to-telomere genome assembly of Cryptosporidium parvum IOWA, annotated with reference gene IDs and RNA evidence.

Long-read assembly and comparative evidence-based reanalysis of Cryptosporidium genome sequences reveal new biological insights

The paper presents a new high-quality genome assembly and annotation for Cryptosporidium parvum IOWA, revealing structural and functional insights into its genome and evolutionary relationships with related species.

A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia

The paper reports a novel fragmented mitochondrial genome in Toxoplasma gondii and related tissue coccidia, revealing a unique genome architecture and cytochrome gene structure.

Stage-Specific Long Non-coding RNAs in Cryptosporidium parvum as Revealed by Stranded RNA-Seq

This study identifies 396 novel lncRNAs in Cryptosporidium parvum using RNA-seq, showing differential expression and potential regulatory roles.