Adam Frankish

GBZ-base and GAF-base: Indexed pangenome file formats

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

Apollo 3: Multi-Species Genome Curation

Apollo 3 is a new manual genome annotation tool that integrates with JBrowse 2, enabling multi-genome editing and synteny visualization.

HPRC2: A human pangenome reference with near-complete coverage of common genetic variation

460 haplotypes from 230 genomes, selected to maximize common-variant coverage, capture 99.43% of All of Us common small variants and halve structurally unreliable regions and base errors versus HPRC1.

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion.

The paper analyzes chromosome 22q11.2 haplotypes to show how structural variations in specific regions correlate with microdeletion and inversion risks across populations.

Pangenome discovery of missing autism variants

The paper uses long-read sequencing to identify pathogenic variants in autism cases, finding three pathogenic mutations and nine candidate structural variants missed by short-read sequencing.

Exploring penetrance of clinically relevant variants in over 800,000 humans from the Genome Aggregation Database

The paper analyzes over 800,000 human genomes to assess penetrance of clinically relevant variants, finding that 95% of pLoF variants in severe diseases have explanations for lack of disease manifestation.

Transcriptome Universal Single-isoform COntrol: A Framework for Evaluating Transcriptome reconstruction Quality

The paper introduces TUSCO, a framework for evaluating transcriptome reconstruction quality using long-read sequencing by assessing precision and sensitivity with a curated set of single-isoform genes.

An expanded reference catalog of translated open reading frames for biomedical research

The paper expands and refines a reference catalog of human non-canonical open reading frames (ncORFs) by incorporating more datasets and introducing a translation signature score framework to prioritize high-quality ncORFs.

Widespread variation in molecular interactions and regulatory properties among transcription factor isoforms

The paper identifies two categories of transcription factor isoforms with distinct molecular functions and shows they contribute to gene regulatory complexity.

The GENCODE CLS project: massively expanding the lncRNA catalog through capture long-read RNA sequencing

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

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.

Pangenome Graph Construction from Genome Alignment with Minigraph-Cactus

The paper introduces Minigraph-Cactus, a pangenome pipeline that constructs pangenome graphs directly from whole-genome alignments, demonstrating improved performance in mapping and variant calling across human and Drosophila data.

A Draft Human Pangenome Reference

The paper presents a draft human pangenome reference that improves variant discovery and structural variant detection compared to existing references.

Recombination between heterologous human acrocentric chromosomes

The paper shows recombination between heterologous human acrocentric chromosomes using pangenome data, revealing pseudo-homologous regions linked to Robertsonian translocations.

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

This paper outlines a community-driven initiative to create a consolidated catalog of human Ribo-seq ORFs, addressing the lack of standardized annotation for these features.

The Ensembl COVID-19 resource: Ongoing integration of public SARS-CoV-2 data

The paper describes the Ensembl COVID-19 resource, which integrates SARS-CoV-2 genomic data and variant annotations to support research on virus variants and their impact on therapeutics and vaccines.

Cell-type, single-cell, and spatial signatures of brain-region specific splicing in postnatal development

The paper identifies brain-region specific splicing patterns at single-cell and spatial resolution in postnatal mice, revealing cell-type specific and region-specific isoform expression.

Expert Curation of the Human and Mouse Olfactory Receptor Gene Repertoires Identifies Conserved Coding Regions Split Across Two Exons

Cell type specific novel lincRNAs and circRNAs in the BLUEPRINT haematopoietic transcriptomes atlas.

The paper identifies novel long non-coding RNAs and circular RNAs in hematopoietic cells using BLUEPRINT consortium data, highlighting their cell type specificity.

Systematic re-annotation of 191 genes associated with early-onset epilepsy unmasks de novo variants linked to Dravet syndrome in novel SCN1A exons

The paper updates gene annotations for 191 epilepsy genes, reclassifying variants and identifying new de novo SCN1A variants in Dravet syndrome patients.

Novel autoregulatory cases of alternative splicing coupled with nonsense-mediated mRNA decay

The paper identifies novel autoregulatory feedback loops where RNA-binding proteins regulate their own expression via alternative splicing and nonsense-mediated mRNA decay.

Pseudogenes in the mouse lineage: transcriptional activity and strain-specific history

The paper annotates pseudogenes in the mouse genome and strains, finding similar overall characteristics to humans but distinct age distributions and transcriptional patterns.

Nearly all new protein-coding predictions in the CHESS database are not protein-coding

The paper reanalyzes the CHESS database's new protein-coding predictions and finds most are false positives due to homology errors and lack of experimental evidence.

Multiple laboratory mouse reference genomes define strain specific haplotypes and novel functional loci

The paper presents full-length de novo genome assemblies for 16 inbred mouse strains, identifying strain-specific haplotypes and novel functional loci, including a large unannotated gene with potential developmental roles.

High-throughput annotation of full-length long noncoding RNAs with Capture Long-Read Sequencing

The paper introduces RNA Capture Long Seq (CLS) to annotate full-length lncRNAs with high throughput and accuracy, doubling annotated complexity compared to short-read methods.