Eric Christian Rouchka

The paper uses long-read sequencing to analyze proviral variation in lentiviral vector-transduced CAR T cells, finding deletions and mutations affecting transgene function.

The paper introduces HIV SMRTcap, a method for characterizing HIV-1 reservoirs by identifying integration sites and proviral integrity using long-read sequencing, and validates its performance across subtypes and tissue samples.

This paper evaluates how data integration affects persistent homology clustering and biological signal detection in scRNA-seq data, showing topological methods can help distinguish biological patterns from batch noise.

The paper analyzes gene expression and alternative splicing in MS using RNA-seq data to identify differentially expressed genes, spliced transcripts, and SNVs associated with disease pathways and potential therapeutic targets.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

The paper analyzes SNVs in G4-forming regions across databases to identify their impact on G4 structure and disease associations.

The paper constructs a searchable database of RNA-Seq data from spinal cord injury experiments to enable cross-study and cross-species analysis.

The paper classifies G-quadruplex sequences into families using computational methods and annotates them based on sequence, structure, and functional properties.

This study shows that Shoc2 regulates neural crest development by modulating extracellular matrix gene expression and that its loss causes ECM imbalance linked to NSLH.

This paper identifies G-quadruplex forming sequences in three manatee papillomaviruses using computational and biophysical analysis, suggesting their regulatory role in viral function.

The paper presents a framework for reanalyzing Affymetrix GeneChip data using functional regions of interest, improving probe mapping and detection of gene expression changes.

The paper identifies dose-dependent transcriptional biomarkers in peripheral blood lymphocytes exposed to ionizing radiation using microarray analysis.

The paper identifies successful mentoring communities by analyzing mentor-mentee relationships among Nobel laureates using network analysis.