Thomas Derrien

This paper benchmarks circRNA detection tools using a simulation framework and finds they vary in performance, with limited overlap in detected circRNAs and significant computational efficiency differences.

This study introduces ANNEXA, a pipeline that improves genome annotation using long-read RNA sequencing and deep learning, identifying novel genes and transcripts in human and canine cancer cell lines.

The paper assembles a Great Dane genome using long-read sequencing, revealing improvements over the Boxer-derived reference and highlighting retrotransposon activity in canine genetic variation.

This study identifies common genetic risk loci for hematopoietic cancers in dogs and humans by combining GWAS, sequencing, and imputation across breeds and cancers.

This study detects circulating tumor DNA in dogs with cancer, showing its potential as a biomarker for diagnosis and monitoring treatment response in specific cancers.

The paper compares nanopore RNA-Seq and cDNA-Seq for transcriptome profiling in mouse brain and liver, finding that nanopore RNA-Seq is more efficient but cDNA-Seq introduces bias due to read truncation.

The paper annotates transcriptomes and chromatin structures in liver and T cells from four livestock species using RNA-seq, ATAC-seq, and Hi-C, revealing conserved regulatory elements and genome organization patterns.

The paper characterizes canine lncRNAs across 26 tissues, identifies tissue-specific expression patterns, and links them to transposable elements and conserved human lncRNAs.

This study shows that the green peach aphid uses rapid transcriptional changes of duplicated genes to colonize diverse host plants without genetic specialization.

FEELnc annotates long non-coding RNAs and mRNAs in the dog transcriptome, identifying 10,374 novel lncRNAs and 58,640 new mRNA transcripts.