Leo Goodstadt

Leo Goodstadt
University of Oxford | OX · Wellcome Trust Centre for Human Genetics

About

195
Publications
58,530
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27,012
Citations
Citations since 2016
19 Research Items
7241 Citations
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201620172018201920202021202202004006008001,0001,200
201620172018201920202021202202004006008001,0001,200
201620172018201920202021202202004006008001,0001,200

Publications

Publications (195)
Article
Full-text available
We report full-length draft de novo genome assemblies for 16 widely used inbred mouse strains and find extensive strain-specific haplotype variation. We identify and characterize 2,567 regions on the current mouse reference genome exhibiting the greatest sequence diversity. These regions are enriched for genes involved in pathogen defence and immun...
Preprint
Full-text available
The most commonly employed mammalian model organism is the laboratory mouse. A wide variety of genetically diverse inbred mouse strains, representing distinct physiological states, disease susceptibilities, and biological mechanisms have been developed over the last century. We report full length draft de novo genome assemblies for 16 of the most w...
Article
Two bottlenecks impeding the genetic analysis of complex traits in rodents are access to mapping populations able to deliver gene-level mapping resolution and the need for population-specific genotyping arrays and haplotype reference panels. Here we combine low-coverage (0.15×) sequencing with a new method to impute the ancestral haplotype space in...
Data
Relationship between variation in transcription and a variable cluster of DHS peaks. Chromosomal positions are shown in kilobases. The density of aligned DHS-seq reads in a moving 300 bp window, with a 30 bp increment is shown for each mouse strain. The poly(A)− transcription from each strain is displayed (in blue) as the aligned read depth per bas...
Data
Full-text available
Effect of altering parameters in the peak finding algorithm on the detection of variable peaks. The two parameters are the window size (in kilobases), shown on the horizontal axis, and the stringency (p), shown for values between 2 and 8 as a set of coloured lines. The vertical axis shows the percentage of variable sites, as calculated using a 5% F...
Data
Full-text available
Closest distance from a variable DHS to a significantly associated sequence variant. The horizontal axis shows the distance in kilobases (Kb) from each of the 1,397 variable DHS to a sequence variant that is associated at a 5% FDR. The P-value is calculated by associating the strain distribution pattern of the DHS with the strain distribution seque...
Data
Table of variable DHS and associated features. The 1,397 peaks are categorized into three classes: I discrete simple; II discrete compound; III continuous quantitative variation. The table provides results from analysis of matches to regions of sequence conservation, to regions identified as enhancers and promoters (is.enh and is.promoter), and the...
Article
Full-text available
Variation at regulatory elements, identified through hypersensitivity to digestion by DNase I, is believed to contribute to variation in complex traits, but the extent and consequences of this variation are poorly characterized. Analysis of terminally differentiated erythroblasts in eight inbred strains of mice identified reproducible variation at...
Article
Full-text available
The Collaborative Cross Consortium reports here on the development of a unique genetic resource population. The Collaborative Cross (CC) is a multi parental recombinant inbred panel derived from eight laboratory mouse inbred strains. Breeding of the CC lines was initiated at multiple international sites using mice from The Jackson Laboratory. Curre...
Article
Full-text available
We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten times more variants than previously known. We use these genomes to explore the phylogenetic history of the laboratory mouse and to examine the functional consequences of allele-specific variation on transcript abundance, revealing that at least 12% of transcr...
Article
Full-text available
Structural variation is widespread in mammalian genomes and is an important cause of disease, but just how abundant and important structural variants (SVs) are in shaping phenotypic variation remains unclear. Without knowing how many SVs there are, and how they arise, it is difficult to discover what they do. Combining experimental with automated a...
Article
Full-text available
The Collaborative Cross (CC) is a genetic reference panel of recombinant inbred lines of mice, designed for the dissection of complex traits and gene networks. Each line is independently descended from eight genetically diverse founder strains such that the genomes of the CC lines, once fully inbred, are fine-grained homozygous mosaics of the found...
Article
Full-text available
An official journal of the Genetics Society, Heredity publishes high-quality articles describing original research and theoretical insights in all areas of genetics. Research papers are complimented by News & Commentary articles and reviews, keeping researchers and students abreast of hot topics in the field.
Article
Full-text available
Computational pipelines are common place in scientific research. However, most of the resources for constructing pipelines are heavyweight systems with graphical user interfaces. Ruffus is a library for the creation of computational pipelines. Its lightweight and unobtrusive design recommends it for use even for the most trivial of analyses. At the...
Article
Full-text available
Long considered to be the building block of life, it is now apparent that protein is only one of many functional products generated by the eukaryotic genome. Indeed, more of the human genome is transcribed into noncoding sequence than into protein-coding sequence. Nevertheless, whilst we have developed a deep understanding of the relationships betw...
Data
Full-text available
Table S1: genome coordinates used in multi-species sequence alignments. Table S2: PCR primers used for amplification of in situ hybridization probes and 3' and 5' lncRNA ortholog RACE.
Data
Full-text available
Figure S1: splice-site and poly(A)-signal conservation among AK043754, AK082072, and AK082467 orthologs. Figure S2: sense probe controls for in situ hybridization.
Data
Multiple sequence alignment (shaded according to a 90% consensus) of Prdm9 zinc finger sequences from the sea anemone, Nematostella vectensis. These form part of a predicted gene (NEMVEDRAFT_v1g113856) that has been predicted from scaffold_120 of the N. vectensis v.1.0 genome assembly (Joint Genome Institute). (2.64 MB EPS)
Data
Multiple sequence alignment (shaded according to a 90% consensus) of 23 Lottia gigantea Prdm9 zinc finger sequences. These have been predicted from scaffold 11 (bases 1507994-1510370) of the Lottia genome assembly (v1.0) produced by the Joint Genome Institute. This gene prediction is supported by an expressed sequence tag from L. gigantea male gona...
Data
Multiple sequence alignment (shaded according to a 90% consensus) of Prdm9 zinc finger sequences from the Atlantic salmon (Salmo salar; accession ACN10800, supported by ESTs CX352799, GE785155, EG785159, and EG785158) and from the Pacific Ocean rainbow trout (Oncorhynchus mykiss; contig generated from ESTs CR372724, CX253406 1305997, CX253405, CX25...
Data
Phylogenetic tree of rodent Prdm9 zinc finger nucleotide sequences as inferred by phyml [76] version 3.0 (http://www.atgc-montpellier.fr/phyml/) and drawn using FigTree (http://tree.bio.ed.ac.uk/software/figtree). Zinc fingers are numbered sequentially from the C-terminal array. The exceptions are zinc fingers from the mouse and rat, whose numbers...
Data
Multiple sequence alignment (shaded according to a 90% consensus) of 11 Capitella sp.I Prdm9 zinc finger sequences. These have been predicted from scaffold_236 of the Capitella sp.I v.1.0 genome assembly (Joint Genome Institute). (2.95 MB EPS)
Data
Genbank accessions for rodent and human sequences (0.04 MB DOC)
Data
Multiple sequence alignment (shaded according to a 90% consensus) of Prdm9 zinc finger sequences from the water vole (Arvicola terrestris) and field vole (Microtus agrestis). (2.75 MB EPS)
Data
Full-text available
Multiple sequence alignment of Prdm9 zinc fingers from all analysed species in FASTA format. (0.09 MB PDF)
Article
Full-text available
The onset of prezygotic and postzygotic barriers to gene flow between populations is a hallmark of speciation. One of the earliest postzygotic isolating barriers to arise between incipient species is the sterility of the heterogametic sex in interspecies' hybrids. Four genes that underlie hybrid sterility have been identified in animals: Odysseus,...
Article
Full-text available
To take full advantage of the mouse as a model organism, it is essential to distinguish lineage-specific biology from what is shared between human and mouse. Investigations into shared genetic elements common to both have been well served by the draft human and mouse genome sequences. More recently, the virtually complete euchromatic sequences of t...
Article
Full-text available
The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer...
Article
The mouse (Mus musculus) is the premier animal model for understanding human disease and development. Here we show that a comprehensive understanding of mouse biology is only possible with the availability of a finished, high-quality genome assembly. The finished clone-based assembly of the mouse strain C57BL/6J reported here has over 175,000 fewer...