Ian T. Fiddes

This study identifies a missense mutation in the furinb gene in zebrafish that causes hepatic cysts by disrupting ER homeostasis and mTOR signaling during liver development.

This paper expands genome benchmarking to include difficult-to-map regions using linked and long reads, identifying more false negatives in variant calling.

A gapless 3.055 billion bp human genome from HiFi and ultra-long nanopore reads resolves all centromeric arrays and acrocentric p-arms, adding 182 Mbp of new sequence.

BioCantor provides a Python library for genomic feature arithmetic across multiple coordinate systems, offering interoperable support and I/O for various file formats.

scHLAcount computes allele-specific HLA expression from single-cell RNA-seq data, revealing cell-type and tumor-normal differences in allelic patterns.

This paper introduces a method to directly capture CRISPR guides in single-cell RNA-sequencing libraries, enhancing Perturb-seq scalability and enabling multi-omic measurements.

The paper uses single-cell sequencing of genomic DNA to resolve sub-clonal heterogeneity in the COLO829 cell line, identifying four major sub-clones and explaining conflicting bulk sequencing results.

Genome in a Bottle benchmark of 12745 sequence-resolved insertions and deletions of 50 bp or more, integrating 19 calling methods, scores false negatives and false positives alike.

The paper generates a new de novo genome assembly for C57BL/6J Eve, addressing genetic drift in the reference strain and improving genomic accuracy.

This paper introduces Linked-Reads as a method to comprehensively analyze genome variation, showing it can detect both small and large variants and reconstruct haplotypes more effectively than short-read sequencing.

The paper uses chimpanzee cerebral organoids to identify human-specific genes in cortical development and finds increased PI3K/AKT/mTOR activation in human outer radial glia.

This paper links subclonal mutations to transcriptional profiles in AML using integrated single-cell RNA-sequencing and whole genome sequencing.

This study identifies 169 differentially expressed genes in black bear kidneys during hibernation, highlighting potential mechanisms for avoiding kidney damage.

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

The paper introduces CAT, a toolkit for simultaneous clade and personal genome annotation, demonstrating its ability to discover novel genes and improve cross-species RNA expression analysis.

The paper identifies human-specific NOTCH2NL genes linked to neurodevelopmental disorders and shows they affect cortical neurogenesis through Notch signaling.

The paper presents an updated horse reference genome, EquCab3, which improves contiguity and composition compared to the previous version, EquCab2.

The paper compares genome assemblies of Mus caroli and Mus pahari with Mus musculus and Rattus norvegicus to reveal lineage-specific evolutionary mechanisms, particularly repeat-associated processes.

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.

Nanopore-only sequencing of GM12878 across 39 MinION flowcells (91.2 Gb) yielded an assembly with NG50 ∼3 Mb; adding 5× ultra-long reads raised NG50 to 6.4 Mbp.