William Chow

Designing AI-programmable therapeutics with the EDEN family of foundation models

This paper introduces the EDEN family of foundation models for AI-programmable therapeutic design, demonstrating their ability to generate functional gene insertions, antibiotic peptides, and synthetic microbiomes.

Breaking Through Biology's Data Wall: Expanding the Known Tree of Life by Over 10x using a Global Biodiscovery Pipeline

The paper introduces BaseData, a new biological sequence database that expands known protein diversity by over 10x using a global biodiscovery pipeline.

A revamped rat reference genome improves the discovery of genetic diversity in laboratory rats

The paper presents an improved rat reference genome, mRatBN7.2, which enhances genomic, transcriptomic, and proteomics data mapping and identifies millions of genetic variations across rat strains.

Genomics of cold adaptations in the Antarctic notothenioid fish radiation.

The paper generates and analyzes genome assemblies for 24 Antarctic notothenioid fish species to study cold adaptations, identifying genomic changes related to antifreeze proteins and haemoglobin loss.

Differential sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

The paper analyzes genomes of leatherback and green turtles to identify gene family expansions and demographic differences that may influence their ecological adaptations and conservation status.

Pangenomics provides insights into the role of synanthropy in barn swallow evolution

The paper presents a pangenome for the barn swallow and identifies genes under selection linked to synanthropy and domestication traits.

A haplotype-resolved genome assembly of the Nile rat facilitates exploration of the genetic basis of diabetes

This paper presents a haplotype-resolved genome assembly of the Nile rat, revealing unique genomic features relevant to type 2 diabetes and metabolic dysfunctions.

Genome sequence assembly evaluation using long-range sequencing data

This paper introduces Asset, a tool to evaluate genome assemblies using long-range data, demonstrating its ability to detect structural misassemblies in human, goat, and fish genomes.

The swan genome and transcriptome: its not all black and white

The paper generates the first chromosome-length annotated genomes and transcriptomes of black and mute swans, revealing immune system limitations and plumage-related genetic differences.

The complete sequence of a human genome

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.

A high-quality Genome and Comparison of Short versus Long Read Transcriptome of the Palaearctic duck Aythya fuligula (Tufted Duck)

The paper presents a high-quality genome and transcriptome of the tufted duck, comparing short and long-read sequencing technologies for transcriptome assembly.

A Chromosome-level Genome Assembly of the Reed Warbler (Acrocephalus scirpaceus)

The paper presents a high-quality chromosome-level genome assembly of the reed warbler and identifies two macrochromosomal fusions.

Towards complete and error-free genome assemblies of all vertebrate species

The paper summarizes methods and lessons from assembling 16 vertebrate genomes, highlights the importance of long-read sequencing, and introduces the Vertebrate Genomes Project to generate complete reference genomes for all vertebrate species.

Significantly improving the quality of genome assemblies through curation

gEVAL-assisted manual curation of 111 VGP and DToL assemblies averaged 221 interventions per Gb, raising mean scaffold N50 by 40% and cutting scaffold counts by 29%.

Reference genome and demographic history of the most endangered marine mammal, the vaquita

The paper generates a high-quality reference genome for the vaquita and analyzes its demographic history, revealing long-term population stability and low genetic diversity.

Telomere-to-telomere assembly of a complete human X chromosome

The paper presents a gapless, telomere-to-telomere assembly of the human X chromosome using ultra-long-read nanopore sequencing and complementary technologies.

An improved pig reference genome sequence to enable pig genetics and genomics research

The paper presents improved pig reference genomes using long-read sequencing, enhancing continuity and accuracy for pig genetics and genomics research.

Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

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.

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.

gEVAL - A web based browser for evaluating genome assemblies

gEVAL is a web browser for evaluating genome assemblies by comparing them to datasets and highlighting errors and areas for improvement.

The pig X and Y chromosomes: structure, sequence and evolution

This paper presents improved assemblies and gene annotations for the pig X and Y chromosomes, revealing evolutionary mechanisms and gene content differences compared to other mammals.