Benjamin D. Rosen
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View article: Insights into natural neocentromere evolution from a cattle T2T X chromosome
Insights into natural neocentromere evolution from a cattle T2T X chromosome Open
The cattle genome is crucial for understanding ruminant biology, but it remains incomplete. Here we present a telomere-to-telomere haplotype-resolved X chromosome and four autosomes of cattle in a near-complete assembly that is 431 Mb (16%…
View article: Inferring Domestic Goat Demographic History Through Ancient Genome Imputation
Inferring Domestic Goat Demographic History Through Ancient Genome Imputation Open
Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limit…
View article: Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens
Bighorn sheep T2T genome assembly reveals differences in immune genes: a potential cause of high morbidity due to respiratory pathogens Open
The bighorn sheep ( Ovis canadensis ), despite its close relation to domestic sheep, suffer higher morbidity and mortality from respiratory disease complexes, likely due to genetic differences in immune responses. Unraveling highly repetit…
View article: Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet
Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet Open
SUMMARY High-quality genome assemblies are essential for understanding speciation, evolution, and for building reference genomes and pan-genomes. Despite major advances in long-read sequencing technologies and graph-based assembly algorith…
View article: Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes
Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes Open
View article: The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression
The genetic diversity of Indonesian cattle has been shaped by multiple introductions and adaptive introgression Open
View article: The Use and Utility of Wearable Devices for Tracking Sleep and Activity in Inpatient Mental Health Settings: Protocol for a Rapid Review (Preprint)
The Use and Utility of Wearable Devices for Tracking Sleep and Activity in Inpatient Mental Health Settings: Protocol for a Rapid Review (Preprint) Open
BACKGROUND Wearable devices offer an opportunity objectively monitor and capture sleep and activity in psychiatric inpatient settings, where traditional approaches often rely on subjective reporting or staff observation which have inheren…
View article: Genomic Analysis of Hair Sheep From West/Central Africa Reveals Unique Genetic Diversity and Ancestral Links to Breed Formation in the Caribbean
Genomic Analysis of Hair Sheep From West/Central Africa Reveals Unique Genetic Diversity and Ancestral Links to Breed Formation in the Caribbean Open
Cameroon Blackbelly sheep are a domestic breed of hair sheep from West/Central Africa. They are popular with small‐holder farmers in Cameroon as they are highly resilient to local environmental challenges and are prolific a‐seasonal breede…
View article: Inferring domestic goat demographic history through ancient genome imputation
Inferring domestic goat demographic history through ancient genome imputation Open
Goats were among the earliest managed animals, making them a natural model to explore the genetic consequences of domestication. However, a challenge in ancient genomic analysis is the relatively low genome coverage for most samples, limit…
View article: Constructing a draft Indian cattle pangenome using short-read sequencing
Constructing a draft Indian cattle pangenome using short-read sequencing Open
Indian desi cattle, known for their adaptability and phenotypic diversity, represent a valuable genetic resource. However, a single reference genome often fails to capture the full extent of their genetic variation. To address this, we con…
View article: Cattle T2T X Chromosome: Insights into Natural Neocentromere Evolution
Cattle T2T X Chromosome: Insights into Natural Neocentromere Evolution Open
The cattle genome is crucial for understanding ruminant biology, but it remains incomplete. The first telomere-to-telomere haplotype-resolved X chromosome and four autosomes of cattle are presented in a near-complete assembly that is 431 M…
View article: Population structure and domestication history of the Javan banteng ( <i>Bos javanicus javanicus</i> )
Population structure and domestication history of the Javan banteng ( <i>Bos javanicus javanicus</i> ) Open
The domestication of the banteng in Southeast Asia is one of the World’s least known livestock domestications, yet a vital component of the agricultural system in Indonesia and surrounding countries. Here we generated the first reference g…
View article: Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle
Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle Open
View article: The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project
The Farm Animal Genotype–Tissue Expression (FarmGTEx) Project Open
Genetic mutation and drift, coupled with natural and human-mediated selection and migration, have produced a wide variety of genotypes and phenotypes in farmed animals. We here introduce the Farm Animal Genotype-Tissue Expression (FarmGTEx…
View article: Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus
Advancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus Open
View article: Genome assemblies of Indian <i>desi</i> cattle reveals hotspots of rearrangements and immune-related genetic diversity
Genome assemblies of Indian <i>desi</i> cattle reveals hotspots of rearrangements and immune-related genetic diversity Open
India, home to the world’s largest cattle population, hosts native dairy breeds essential to its agricultural economy because of their adaptability and resilience. This study characterizes the genomes of five prominent breeds Gir, Kankrej,…
View article: Bighorn Sheep T2T Genome Assembly Reveals Differences in Immune Genes: A Potential Cause of High Morbidity Due to Respiratory Pathogens
Bighorn Sheep T2T Genome Assembly Reveals Differences in Immune Genes: A Potential Cause of High Morbidity Due to Respiratory Pathogens Open
View article: Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content
Telomere-to-telomere assemblies of cattle and sheep Y-chromosomes uncover divergent structure and gene content Open
Reference genomes of cattle and sheep have lacked contiguous assemblies of the sex-determining Y chromosome. Here, we assemble complete and gapless telomere to telomere (T2T) Y chromosomes for these species. We find that the pseudo-autosom…
View article: Constructing a Draft Indian Cattle Pangenome Using Short-Read Sequencing
Constructing a Draft Indian Cattle Pangenome Using Short-Read Sequencing Open
Background Indian cattle known as desi cattle, renowned for their adaptability to harsh environments and diverse phenotypic traits, represent a valuable genetic resource. While reference genome assemblies have been instrumental in advancin…
View article: Genomic analysis of hair sheep from West/Central Africa reveals unique genetic diversity and ancestral links to breed formation in the Caribbean
Genomic analysis of hair sheep from West/Central Africa reveals unique genetic diversity and ancestral links to breed formation in the Caribbean Open
Cameroon Blackbelly sheep are a domestic breed of hair sheep from West/Central Africa. They are popular with small holder farmers in Cameroon as they are highly resilient to local environmental challenges and are prolific aseasonal breeder…
View article: Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans
Systemic interindividual DNA methylation variants in cattle share major hallmarks with those in humans Open
View article: The first complete T2T Assemblies of Cattle and Sheep Y-Chromosomes uncover remarkable divergence in structure and gene content
The first complete T2T Assemblies of Cattle and Sheep Y-Chromosomes uncover remarkable divergence in structure and gene content Open
View article: Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project
Disentangling river and swamp buffalo genetic diversity: initial insights from the 1000 Buffalo Genomes Project Open
More people in the world depend on water buffalo for their livelihoods than on any other domesticated animals, but its genetics is still not extensively explored. The 1000 Buffalo Genomes Project (1000BGP) provides genetic resources for gl…
View article: 52 The Power of Pangenome Assemblies in Ruminants
52 The Power of Pangenome Assemblies in Ruminants Open
High quality reference genomes are the bases of all genomic research and they have facilitated a wealth of discoveries and research tools for the improvement of livestock species. These works have enabled major advances in the fields of an…
View article: Participatory investigation of goat farmers’ breeding practices, trait preference and selection criteria in Burkina Faso
Participatory investigation of goat farmers’ breeding practices, trait preference and selection criteria in Burkina Faso Open
The community-based breeding program (CBBP) is an innovative approach recommended for genetic improvement and sustainable use of animal genetic resources in extensive farming systems. Successful implementation of this approach requires an …
View article: Using the community-based breeding program (CBBP) model as a collaborative platform to develop the African Goat Improvement Network—Image collection protocol (AGIN-ICP) with mobile technology for data collection and management of livestock phenotypes
Using the community-based breeding program (CBBP) model as a collaborative platform to develop the African Goat Improvement Network—Image collection protocol (AGIN-ICP) with mobile technology for data collection and management of livestock phenotypes Open
Introduction: The African Goat Improvement Network Image Collection Protocol (AGIN-ICP) is an accessible, easy to use, low-cost procedure to collect phenotypic data via digital images. The AGIN-ICP collects images to extract several phenot…
View article: The African Goat Improvement Network: a scientific group empowering smallholder farmers
The African Goat Improvement Network: a scientific group empowering smallholder farmers Open
Graphical Abstract
View article: A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other<i>Bos</i>species
A Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other<i>Bos</i>species Open
Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 Chinese indicine cattle across southern Chi…
View article: The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species
The Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species Open
View article: Morphometric Characterization of Local Goat Breeds in Two Agroecological Zones of Burkina Faso, West Africa
Morphometric Characterization of Local Goat Breeds in Two Agroecological Zones of Burkina Faso, West Africa Open
In Burkina Faso, goats are the second most numerous ruminant livestock population, with almost exclusively indigenous breeds being reared in extensive production systems in various agroecological zones. This study was carried out to unders…