Christopher Vollmers

IG-28 identifies and quantifies high-confidence isoforms from large bulk and single-cell full-length cDNA datasets more effectively than existing tools.

The paper adapts R2C2 sequencing for low-cost, rapid plasmid sequencing and introduces Chopper, a pipeline that generates full-length plasmid sequences from Oxford Nanopore data.

This study identifies circadian oscillating isoforms in mouse livers using full-length cDNA reads and provides accessible resources for further research.

The paper identifies splicing deficiency in non-recombining mating-type chromosomes across phytoplankton species, showing how recombination suppression leads to transcript-level dysfunction.

The paper introduces AIR-SPACE, a method combining spatial transcriptomics and immune receptor sequencing to map adaptive immune responses in lymph nodes post-viral infection, revealing spatial dynamics of immune cell activation and differentiation.

This study identifies 38 COPD GWAS loci with evidence of sQTLs, showing that sQTL analysis in whole blood and lung tissue provides novel insights into COPD mechanisms.

The paper introduces R2C2+UMI, a method combining concatemeric consensus sequencing with UMIs to achieve ultra-accurate sequencing of amplicons on Oxford Nanopore sequencers.

The paper develops FLAIR2 to detect haplotype-specific transcript variation using long-read sequencing, revealing ADAR's role in splicing and RNA editing in lung cancer.

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 uses long-read sequencing to study mRNA isoform-specific ribosome association during neuronal differentiation, finding that alternative splicing in coding and untranslated regions affects translational control.

The paper generates a mouse multi-tissue genome annotation atlas using long-read sequencing and the Mandalorion tool, providing tissue-specific transcript isoform information.

Mandalorion v4 improves isoform identification and quantification from full-length transcriptome sequencing data, showing high precision and recall even without genome annotation.

The paper demonstrates that Illumina short-read libraries can be sequenced on the ONT MinION with high accuracy using the R2C2 method, achieving error rates comparable to Illumina MiSeq.

The paper uses R2C2 to sequence full-length cDNA from PBMCs, enabling isoform-level transcriptomes and TCR/BCR sequencing without Illumina data.

The paper identifies a genetic variant in NPNT associated with COPD risk and lung function through splicing analysis using long-read sequencing.

The paper demonstrates a chromosome-scale genome assembly of a single outbred Drosophila melanogaster using a hybrid method with low input DNA.

The paper uses full-length cDNA sequencing to accurately characterize the human immune cell transcriptome, enabling HLA allele typing and adaptive immune receptor repertoire analysis.

The paper depletes hemoglobin transcripts using Long-DASH to improve transcriptome annotation in polar bears, discovering 6,000 high-confidence isoforms and novel genes.

The paper analyzes mountain lion genomes to study genetic rescue effects in inbred populations, finding that translocated individuals quickly lose genetic diversity due to local inbreeding.

R2C2 improves nanopore read accuracy for full-length single-cell cDNA sequencing, enabling more accurate isoform-level transcriptome analysis.

Tn5Prime is a 5' capture method for RNA-seq that enables accurate transcription start site identification and transcriptome quantification in single cells and bulk samples.

The paper uses long-read RNAseq to identify and quantify complex isoforms in individual B cells, revealing widespread transcriptional variation in surface receptors and the antibody heavy chain locus.