Christopher Vollmers
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View article: Spatial Mapping of the Adaptive Immune Receptor Repertoire in Lymph Nodes During Viral Infection 2278
Spatial Mapping of the Adaptive Immune Receptor Repertoire in Lymph Nodes During Viral Infection 2278 Open
Description The spatial organization of adaptive immune cells within lymph nodes is essential for understanding immune responses during infection and disease. Here, we sought to investigate the spatial and temporal changes to the adaptive …
View article: B-cell immune repertoire sequencing in tobacco cigarette smoking, vaping, and chronic obstructive pulmonary disease in the COPDGene cohort
B-cell immune repertoire sequencing in tobacco cigarette smoking, vaping, and chronic obstructive pulmonary disease in the COPDGene cohort Open
Rationale Cigarette smoking (CS) impairs B-cell function and antibody production, increasing infection risk. The impact of e-cigarette use ('vaping') and combined CS and vaping ('dual-use') on B-cell activity is unclear. Objective To exami…
View article: A Temporal and Spatial Atlas of Adaptive Immune Responses in the Lymph Node Following Viral Infection
A Temporal and Spatial Atlas of Adaptive Immune Responses in the Lymph Node Following Viral Infection Open
The spatial organization of adaptive immune cells within lymph nodes is critical for understanding immune responses during infection and disease. Here, we introduce AIR-SPACE, an integrative approach that combines high-resolution spatial t…
View article: Sequencing complete plasmids on Oxford Nanopore Technology Sequencers using <i>R2C2</i> and <i>Chopper</i>
Sequencing complete plasmids on Oxford Nanopore Technology Sequencers using <i>R2C2</i> and <i>Chopper</i> Open
Plasmids are ubiquitous tools in molecular biology which are used for a large variety of experiments within academic and commercial labs. Both new and old plasmids have to undergo sequencing-based analysis to determine whether or not they …
View article: Generation and analysis of a mouse multitissue genome annotation atlas
Generation and analysis of a mouse multitissue genome annotation atlas Open
Generating an accurate and complete genome annotation for an organism is complex because the cells within each tissue can express a unique set of transcript isoforms from a unique set of genes. A comprehensive genome annotation should cont…
View article: The Circadian Isoform Landscape of Mouse Livers
The Circadian Isoform Landscape of Mouse Livers Open
The mammalian circadian clock is an autoregulatory feedback process that is responsible for homeostasis in mouse livers. These circadian processes are well understood at the gene-level, however, not well understood at the isoform-level. To…
View article: B cell immune repertoire sequencing in tobacco cigarette smoking, vaping, and chronic obstructive pulmonary disease in the COPDGene cohort
B cell immune repertoire sequencing in tobacco cigarette smoking, vaping, and chronic obstructive pulmonary disease in the COPDGene cohort Open
Rationale Cigarette smoking (CS) impairs B cell function and antibody production, increasing infection risk. The impact of e-cigarette use (’vaping’) and combined CS and vaping (’dual-use’) on B cell activity is unclear. Objective To exami…
View article: R2C2 + UMI: Combining concatemeric and unique molecular identifier–based consensus sequencing enables ultra-accurate sequencing of amplicons on Oxford Nanopore Technologies sequencers
R2C2 + UMI: Combining concatemeric and unique molecular identifier–based consensus sequencing enables ultra-accurate sequencing of amplicons on Oxford Nanopore Technologies sequencers Open
The sequencing of PCR amplicons is a core application of high-throughput sequencing technology. Using unique molecular identifiers (UMIs), individual amplified molecules can be sequenced to very high accuracy on an Illumina sequencer. Howe…
View article: Detecting haplotype-specific transcript variation in long reads with FLAIR2
Detecting haplotype-specific transcript variation in long reads with FLAIR2 Open
Background RNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants (SNVs) in RNA have been demonst…
View article: Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification Open
View article: Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation
Long-read subcellular fractionation and sequencing reveals the translational fate of full-length mRNA isoforms during neuronal differentiation Open
Alternative splicing (AS) alters the cis -regulatory landscape of mRNA isoforms, leading to transcripts with distinct localization, stability, and translational efficiency. To rigorously investigate mRNA isoform-specific ribosome associati…
View article: Generation and analysis of a mouse multi-tissue genome annotation atlas
Generation and analysis of a mouse multi-tissue genome annotation atlas Open
Generating an accurate and complete genome annotation for an organism is complex because the cells within each tissue can express a unique set of transcript isoforms from a unique set of genes. A comprehensive genome annotation should cont…
View article: R2C2+UMI: Combining concatemeric consensus sequencing with unique molecular identifiers enables ultra-accurate sequencing of amplicons on Oxford Nanopore Technologies sequencers
R2C2+UMI: Combining concatemeric consensus sequencing with unique molecular identifiers enables ultra-accurate sequencing of amplicons on Oxford Nanopore Technologies sequencers Open
The sequencing of PCR amplicons is a core application of high-throughput sequencing technology. Using unique molecular identifiers (UMIs), individual amplified molecules can be sequenced to very high accuracy on an Illumina sequencer. Howe…
View article: Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification Open
The Long-read RNA-Seq Genome Annotation Assessment Project (LRGASP) Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. The consortium generated over 427 million long-read sequences from …
View article: Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion
Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion Open
View article: Detecting haplotype-specific transcript variation in long reads with FLAIR2
Detecting haplotype-specific transcript variation in long reads with FLAIR2 Open
Background RNA-Seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants in RNA have been demonstrated t…
View article: Smar2C2: A Simple and Efficient Protocol for the Identification of Transcription Start Sites
Smar2C2: A Simple and Efficient Protocol for the Identification of Transcription Start Sites Open
Promoters and the noncoding sequences that drive their function are fundamental aspects of genes that are critical to their regulation. The transcription preinitiation complex binds and assembles on promoters where it facilitates transcrip…
View article: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2 Open
High-throughput short-read sequencing has taken on a central role in research and diagnostics. Hundreds of different assays take advantage of Illumina short-read sequencers, the predominant short-read sequencing technology available today.…
View article: Whole-genome sequence and assembly of the Javan gibbon (<i>Hylobates moloch</i>)
Whole-genome sequence and assembly of the Javan gibbon (<i>Hylobates moloch</i>) Open
The Javan gibbon, Hylobates moloch, is an endangered gibbon species restricted to the forest remnants of western and central Java, Indonesia, and one of the rarest of the Hylobatidae family. Hylobatids consist of 4 genera (Holoock, Hylobat…
View article: Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion
Identifying and quantifying isoforms from accurate full-length transcriptome sequencing reads with Mandalorion Open
The Mandalorion tool, which we have continuously developed over the last 5 years, identifies and quantifies high-confidence isoforms from accurate full-length transcriptome sequencing reads produced by methods like PacBio Iso-Seq and ONT-b…
View article: Glacial ice supports a distinct and undocumented polar bear subpopulation persisting in late 21st-century sea-ice conditions
Glacial ice supports a distinct and undocumented polar bear subpopulation persisting in late 21st-century sea-ice conditions Open
Polar bears are susceptible to climate warming because of their dependence on sea ice, which is declining rapidly. We present the first evidence for a genetically distinct and functionally isolated group of polar bears in Southeast Greenla…
View article: Single-cell isoform analysis in human immune cells
Single-cell isoform analysis in human immune cells Open
High-throughput single-cell analysis today is facilitated by protocols like the 10X Genomics platform or Drop-Seq which generate cDNA pools in which the origin of a transcript is encoded at its 5′ or 3′ end. Here, we used R2C2 to sequence …
View article: Additional file 3 of Single-cell isoform analysis in human immune cells
Additional file 3 of Single-cell isoform analysis in human immune cells Open
Additional file 3. Cell type specific isoforms in psl format.
View article: Additional file 2 of Single-cell isoform analysis in human immune cells
Additional file 2 of Single-cell isoform analysis in human immune cells Open
Additional file 2. Supplemental tables 3-4. (XLS 169 kb)
View article: Illumina But With Nanopore: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
Illumina But With Nanopore: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2 Open
High-throughput short-read sequencing has taken on a central role in research and diagnostics. Hundreds of different assays exist today to take advantage of Illumina short-read sequencers, the predominant short-read sequencing technology a…
View article: Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
Systematic assessment of long-read RNA-seq methods for transcript identification and quantification Open
With increased usage of long-read sequencing technologies to perform transcriptome analyses, there becomes a greater need to evaluate different methodologies including library preparation, sequencing platform, and computational analysis to…
View article: ENCSR259DBL
ENCSR259DBL Open
View article: ENCSR472FCO
ENCSR472FCO Open
View article: ENCSR602SAJ
ENCSR602SAJ Open
View article: ENCSR096PNA
ENCSR096PNA Open