Kerstin Howe
A5049934769- Genomics and Phylogenetic Studies
- Chromosomal and Genetic Variations
- Genetic diversity and population structure
- Genetic Mapping and Diversity in Plants and Animals
- RNA and protein synthesis mechanisms
- Genetics, Bioinformatics, and Biomedical Research
- Identification and Quantification in Food
- Genomics and Chromatin Dynamics
- Genetic and Clinical Aspects of Sex Determination and Chromosomal Abnormalities
- Genomic variations and chromosomal abnormalities
- Genetic and phenotypic traits in livestock
- Animal Genetics and Reproduction
- CRISPR and Genetic Engineering
- DNA and Biological Computing
- Marine animal studies overview
- Aquaculture disease management and microbiota
- Environmental DNA in Biodiversity Studies
- Molecular Biology Techniques and Applications
- Animal Behavior and Reproduction
- Epigenetics and DNA Methylation
- Machine Learning in Bioinformatics
- interferon and immune responses
- Zebrafish Biomedical Research Applications
- Biological Research and Disease Studies
- Bat Biology and Ecology Studies
Wellcome Sanger Institute
2016-2025
ORCID
2021
University of Edinburgh
2020
Aarhus University
2020
Yale University
2017-2018
Max Planck Institute for Developmental Biology
2013
London Women's Clinic
2010
University College London
2010
A high-quality sequence assembly of the zebrafish genome reveals largest gene set any vertebrate and provides information on key genomic features, comparison to human reference shows that approximately 70% protein-coding genes have at least one clear orthologue. The — a model organism for study development disease has now been sequenced published as well-annotated genome. Zebrafish turns out so far sequenced, few pseudogenes. Importantly studies, between sequences obvious second paper...
Since its initial release in 2000, the human reference genome has covered only euchromatic fraction of genome, leaving important heterochromatic regions unfinished. Addressing remaining 8% Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion–base pair sequence T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors prior references, and introduces nearly 200 million base pairs containing 1956 gene predictions, 99 which are predicted to be...
Abstract Motivation Rapid development in long-read sequencing and scaffolding technologies is accelerating the production of reference-quality assemblies for large eukaryotic genomes. However, haplotype divergence regions high heterozygosity often results assemblers creating two copies rather than one copy a region, leading to breaks contiguity compromising downstream steps such as gene annotation. Several tools have been developed resolve this problem. they either focus only on removing...
For 10,000 years pigs and humans have shared a close complex relationship. From domestication to modern breeding practices, shaped the genomes of domestic pigs. Here we present assembly analysis genome sequence female Duroc pig (Sus scrofa) comparison with wild from Europe Asia. Wild emerged in South East Asia subsequently spread across Eurasia. Our results reveal deep phylogenetic split between European Asian boars ∼1 million ago, selective sweep indicates selection on genes involved RNA...
Abstract Genome sequence assemblies provide the basis for our understanding of biology. Generating error-free is therefore ultimate, but sadly still unachieved goal a multitude research projects. Despite ever-advancing improvements in data generation, assembly algorithms and pipelines, no automated approach has so far reliably generated near genome eukaryotes. Whilst working towards improved datasets fully evaluation curation actively used to bridge this shortcoming significantly reduce...
The human reference genome assembly plays a central role in nearly all aspects of today's basic and clinical research. GRCh38 is the first coordinate-changing update since 2009; it reflects resolution roughly 1000 issues encompasses modifications ranging from thousands single base changes to megabase-scale path reorganizations, gap closures, localization previously orphaned sequences. We developed new approach sequence generation for targeted updates used data mapping technologies haplotype...
After two decades of improvements, the current human reference genome (GRCh38) is most accurate and complete vertebrate ever produced. However, no single chromosome has been finished end to end, hundreds unresolved gaps persist1,2. Here we present a assembly that surpasses continuity GRCh382, along with gapless, telomere-to-telomere chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing hydatidiform mole CHM13 genome, combined complementary technologies for...
The Ensembl project (http://www.ensembl.org) is a comprehensive genome information system featuring an integrated set of annotation, databases, and other for chordate, selected model organism disease vector genomes. As release 51 (November 2008), fully supports 45 species, three additional species have preliminary support. New in the past year include orangutan six low coverage mammalian Major additions improvements to since our previous report major redesign website; generation multiple...
The Ensembl (http://www.ensembl.org/) project provides a comprehensive and integrated source of annotation chordate genome sequences. Over the past year number genomes available from has increased 15 to 33, with addition sites for mammalian elephant, rabbit, armadillo, tenrec, platypus, pig, cat, bush baby, common shrew, microbat european hedgehog; fish stickleback medaka second example sea squirt (Ciona savignyi) mosquito (Aedes aegypti). Some major features added during include first...
Abstract Here the Human Pangenome Reference Consortium presents a first draft of human pangenome reference. The contains 47 phased, diploid assemblies from cohort genetically diverse individuals 1 . These cover more than 99% expected sequence in each genome and are accurate at structural base pair levels. Based on alignments assemblies, we generate that captures known variants haplotypes reveals new alleles structurally complex loci. We also add 119 million pairs euchromatic polymorphic...
I have read the journal's policy and following conflicts: Paul Flicek is married to deputy editor of PLoS Medicine, Melissa Norton. Evan Eichler on board Pacific Biosciences. Support for this work came from Intramural Research Program NIH, The National Library European Molecular Biology Laboratory, Wellcome Trust (grant number 077198), Howard Hughes Medical Institute (EEE). funders had no role in study design, data collection analysis, decision publish or preparation manuscript.
Abstract Motivation: For most research approaches, genome analyses are dependent on the existence of a high quality reference assembly. However, local accuracy an assembly remains difficult to assess and improve. The gEVAL browser allows user interrogate in any region by comparing it different datasets evaluating concordance. These include: wide variety sequence alignments, comparative multiple assemblies, consistency with optical other physical maps. highlights allelic variations, regions...
We report evidence for a mechanism the maintenance of long-range conserved synteny across vertebrate genomes. found largest mammal-teleost chromosomal segments to be spanned by highly noncoding elements (HCNEs), their developmental regulatory target genes, and phylogenetically functionally unrelated “bystander” genes. Bystander genes are not specifically under control that drive expressed in patterns different from those Reporter insertions distal zebrafish pax6.1/2 , rx3 id1 fgf8 miRNA...
The Vertebrate Genome Annotation (Vega) database ( http://vega.sanger.ac.uk ) was first made public in 2004 and has been designed to view manual annotation of human, mouse zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute. Since its initial release, number human annotated loci more than doubled close 33 000 now contains comprehensive on 20 24 chromosomes, four whole chromosomes around 40% Danio rerio genome. In addition, we offer a haplotype regions comparative...
Abstract Background The domestic pig (Sus scrofa) is important both as a food source and biomedical model given its similarity in size, anatomy, physiology, metabolism, pathology, pharmacology to humans. draft reference genome (Sscrofa10.2) of purebred Duroc female established using older clone-based sequencing methods was incomplete, unresolved redundancies, short-range order orientation errors, associated misassembled genes limited utility. Results We present 2 annotated highly contiguous...
Ensembl(http://www.ensembl.org)integrates genomic information for a comprehensive set of chordate genomes with particular focus on resources human, mouse, rat, zebrafish and other high-value sequenced genomes.We provide complete gene annotations all supported species in addition to specific that target genome variation, function evolution.Ensembl data is accessible variety formats including via our browser, API BioMart.This year marks the tenth anniversary Ensembl time project has grown...
Abstract The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits continuation sequence assembly improvement efforts. We present new version chicken genome (Gallus_gallus-5.0; GCA_000002315.3), built from combined long single molecule sequencing technology, finished BACs, improved physical maps. In overall assembled bases, we see gain 183 Mb, including 16.4 Mb in placed chromosomes with corresponding percentage intact repeat elements characterized. Of...
We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. identify characterize 2,567 regions on the current reference exhibiting greatest sequence diversity. These are enriched genes involved in pathogen defence immunity exhibit enrichment of transposable elements signatures recent retrotransposition events. Combinations alleles unique to an individual strain commonly observed at these loci,...
The kākāpō is a flightless parrot endemic to New Zealand. Once common in the archipelago, only 201 individuals remain today, most of them descending from an isolated island population. We report first genome-wide analyses species, including high-quality genome assembly for kākāpō, one chromosome-level reference genomes sequenced by Vertebrate Genomes Project (VGP). also and analyzed 35 modern sole surviving population 14 extinct mainland While theory suggests that such small likely have...
Abstract In 2001, Celera Genomics and the International Human Genome Sequencing Consortium published their initial drafts of human genome, which revolutionized field genomics. While these updates that followed effectively covered euchromatic fraction heterochromatin many other complex regions were left unfinished or erroneous. Addressing this remaining 8% Telomere-to-Telomere (T2T) has finished first truly complete 3.055 billion base pair (bp) sequence a representing largest improvement to...
Abstract The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society 1,2 . However, it still many gaps and errors, does not represent biological genome as is blend multiple individuals 3,4 Recently, telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but derived from hydatidiform mole cell line nearly homozygous 5 To address these limitations, Human Pangenome...
Abstract Egg-laying mammals (monotremes) are the only extant mammalian outgroup to therians (marsupial and eutherian animals) provide key insights into evolution 1,2 . Here we generate analyse reference genomes of platypus ( Ornithorhynchus anatinus ) echidna Tachyglossus aculeatus ), which represent two monotreme lineages. The nearly complete genome assembly has anchored almost entire onto chromosomes, markedly improving continuity gene annotation. Together with our sequence, species allow...
Abstract The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats extended segmental duplications 1,2 . Although resolution these regions in first complete assembly a genome—the Telomere-to-Telomere Consortium’s CHM13 (T2T-CHM13)—provided model their homology 3 , it remained unclear whether patterns were ancestral or maintained by ongoing recombination exchange. Here we show that contain...