Kristoffer Vitting‐Seerup

AI supported in silico screening of chimeric antigen receptor therapy targets

The paper presents a framework integrating AI and computational tools to evaluate CAR target characteristics, using HER2 as a case study to identify liabilities beyond conventional expression analysis.

IsoformSwitchAnalyzeR v2: Analysis of Functional Isoform Changes in Long-read and Single-cell Sequencing Data

IsoformSwitchAnalyzeR v2 identifies and analyzes functional isoform switches in long-read and single-cell sequencing data, showing disease-relevant changes in Alzheimer's and glioblastoma.

Beyond the Gene in Genetics: How Isoform-Resolved Analysis Empowers the Study of Both Common and Rare Genetic Variation

This study shows that analyzing genetic variants at the isoform level reveals significant associations with human phenotypes and rare variants, highlighting the importance of isoform-resolved analysis in genetics.

Building flexible and robust analysis frameworks for molecular subtyping of cancers

The paper provides a framework for molecular cancer subtyping that integrates quality control, normalization, batch correction, classification, and reporting, with a use case in breast cancer.

Expression and Splicing Mediate Distinct Biological Signals

The paper shows that alternative splicing contributes significantly to biological signals in RNA-seq data, suggesting current studies may miss important insights.

Plasma-derived cell-free DNA methylomes might not enable detection and discrimination of intracranial tumors

This paper critiques a study claiming plasma-derived cell-free DNA methylomes can detect and discriminate intracranial tumors, arguing the evidence is insufficient.

satuRn: Scalable Analysis of differential Transcript Usage for bulk and single-cell RNA-sequencing applications

satuRn analyzes differential transcript usage in bulk and single-cell RNA-seq data, offering scalability and accurate false discovery rate control.

On the Analysis of Transcriptional Noise From RNA-sequencing Data

This paper critiques Varabyou et al.'s simulated RNA-seq data, suggesting improvements in modeling transcriptional noise, particularly splicing noise.

CAGEfightR: Cap Analysis of Gene Expression (CAGE) in R/Bioconductor

CAGEfightR is an R/Bioconductor package for analyzing CAGE data, enabling TSS and enhancer identification, annotation, quantification, and visualization.

IsoformSwitchAnalyzeR: Analysis of changes in genome-wide patterns of alternative splicing and its functional consequences

The paper extends IsoformSwitchAnalyzeR to enable genome-wide analysis of alternative splicing changes and their functional consequences using RNA-seq data from The Cancer Genome Atlas.