Summary This release adds: Genome-alignment support: xPore previously only worked with transcriptome-aligned reads. A new --kmer_source flag on dataprep allows genome-aligned input (handling rever...

A curated list of awesome genomics and bioinformatics agentic skills, MCPs and benchmarks for Claude Code, Copilot, Codex, Cursor, Gemini CLI, etc - GoekeLab/awesome-genomic-skills

Computational Transcriptomics - Third Generation Sequencing - Göke Lab

The Rousseeuw Prize for Statistics is a biennial prize to celebrate outstanding contributions to statistics research.

Nanopore sequencing provides signal data corresponding to the nucleotide motifs sequenced. Through machine learning-based methods, these signals are translated into long-read sequences that overcome t...

A curated list of awesome genomics and bioinformatics agentic skills, MCPs and benchmarks for Claude Code, Copilot, Codex, Cursor, Gemini CLI, etc - GoekeLab/awesome-genomic-skills

Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu - GoekeLab/bambu-pipe

Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu - GoekeLab/bambu-pipe

Computational Transcriptomics - Third Generation Sequencing - Göke Lab

Background Neuropsychiatric disorders are highly complex conditions and the risk of developing a disorder has been tied to hundreds of genomic variants that alter the expression and/or RNA isoforms made by risk genes. However, how these genes contribute to disease risk and onset through altered expression and RNA splicing is not well understood. Results Combining our new bioinformatic pipeline IsoLamp with nanopore long-read amplicon sequencing, we deeply profile the RNA isoform repertoire of 31 high-confidence neuropsychiatric disorder risk genes in Human brain. We show most risk genes are more complex than previously reported, identifying 363 novel isoforms and 28 novel exons, including isoforms which alter protein domains, and genes such as ATG13 and GATAD2A where most expression was from previously undiscovered isoforms. The greatest isoform diversity is detected in the schizophrenia risk gene ITIH4. Mass spectrometry of brain protein isolates confirms translation of a novel exon skipping event in ITIH4, suggesting a new regulatory mechanism for this gene in the brain. Conclusions Our results emphasize the widespread presence of previously undetected RNA and protein isoforms in the human brain and provide an effective approach to address this knowledge gap. Uncovering the isoform repertoire of candidate neuropsychiatric risk genes will underpin future analyses of the functional impact these isoforms have on neuropsychiatric disorders, enabling the translation of genomic findings into a pathophysiological understanding of disease.

Direct RNA-seq in brain reveals RNA isoform and region-specific m6A modifications, highlighting their role in gene regulation.

Gene fusions are found as cancer drivers in diverse adult and pediatric cancers. Accurate detection of fusion transcripts is essential in cancer clinical diagnostics and prognostics and for guiding th...

Single cell CRISPR screens such as Perturb-seq enable transcriptomic profiling of genetic perturbations at scale. However, the data produced by these screens are often noisy due to cost and technical ...

Single cell and spatial transcriptomics have dramatically changed how we can profile RNA from heterogenous biological samples. Combining single cell and spatial profiling with long read RNA-Seq promis...