Jonathan Crabtree
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View article: Author Correction: Complex genetic variation in nearly complete human genomes
Author Correction: Complex genetic variation in nearly complete human genomes Open
View article: Complex genetic variation in nearly complete human genomes
Complex genetic variation in nearly complete human genomes Open
View article: Complex genetic variation in nearly complete human genomes
Complex genetic variation in nearly complete human genomes Open
Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (13…
View article: The Hypervariable Tpr Multigene Family of Theileria Parasites, Defined by a Conserved, Membrane-Associated, C-Terminal Domain, Includes Several Copies with Defined Orthology Between Species
The Hypervariable Tpr Multigene Family of Theileria Parasites, Defined by a Conserved, Membrane-Associated, C-Terminal Domain, Includes Several Copies with Defined Orthology Between Species Open
View article: Parasite control practices on UK stud farms: A client‐based survey
Parasite control practices on UK stud farms: A client‐based survey Open
respectively), the last pH was not different between survivors and non-survivors (median 5.06, 3.77, 7.24 and 6.95, 6.84-7.17respectively).The last pH was significantly lower than the average for survivors (p < 0.05), but not for the non-s…
View article: Understanding UK parasite control practices: A horse owner survey
Understanding UK parasite control practices: A horse owner survey Open
respectively), the last pH was not different between survivors and non-survivors (median 5.06, 3.77, 7.24 and 6.95, 6.84-7.17respectively).The last pH was significantly lower than the average for survivors (p < 0.05), but not for the non-s…
View article: The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain
The Neuroscience Multi-Omic Archive: a BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain Open
Scalable technologies to sequence the transcriptomes and epigenomes of single cells are transforming our understanding of cell types and cell states. The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative Cell…
View article: The Neuroscience Multi-Omic Archive: A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain
The Neuroscience Multi-Omic Archive: A BRAIN Initiative resource for single-cell transcriptomic and epigenomic data from the mammalian brain Open
Scalable technologies to sequence the transcriptomes and epigenomes of single cells are transforming our understanding of cell types and cell states. The Brain Research through Advancing Innovative Neurotechnologies (BRAIN) Initiative Cell…
View article: Mutagenesis of human genomes by endogenous mobile elements on a population scale
Mutagenesis of human genomes by endogenous mobile elements on a population scale Open
Several large-scale Illumina whole-genome sequencing (WGS) and whole-exome sequencing (WES) projects have emerged recently that have provided exceptional opportunities to discover mobile element insertions (MEIs) and study the impact of th…
View article: A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex Open
View article: Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz
Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz Open
The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between microbial communities and a human host might impact an individual’s health or diseas…
View article: Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity
Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity Open
Theileria parva is an economically important, intracellular, tick-transmitted parasite of cattle. A live vaccine against the parasite is effective against challenge from cattle-transmissible T . parva but not against genotypes originating …
View article: HMPDACC: a Human Microbiome Project Multi-omic data resource
HMPDACC: a Human Microbiome Project Multi-omic data resource Open
The Human Microbiome Project (HMP) explored microbial communities of the human body in both healthy and disease states. Two phases of the HMP (HMP and iHMP) together generated >48TB of data (public and controlled access) from multiple, …
View article: Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz
Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz Open
The rich data produced by the second phase of the Human Microbiome Project (iHMP) offers a unique opportunity to test hypotheses that interactions between microbial communities and a human host might impact an individual’s health or diseas…
View article: Capture-based enrichment of<i>Theileria parva</i>DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity
Capture-based enrichment of<i>Theileria parva</i>DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity Open
Theileria parva is an economically important, intracellular, tick-transmitted parasite of cattle. A live vaccine against the parasite is effective against challenge from cattle-transmissible T. parva but not against genotypes originating f…
View article: An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types
An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types Open
Single cell transcriptomics has transformed the characterization of brain cell identity by providing quantitative molecular signatures for large, unbiased samples of brain cell populations. With the proliferation of taxonomies based on ind…
View article: A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina
A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina Open
View article: Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential
Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential Open
View article: Additional file 3. of Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential
Additional file 3. of Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential Open
Description of structural variants. Excel spreadsheet describing structural variants identified in each of the four PfSPZ strain assemblies.
View article: Additional file 5. of Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential
Additional file 5. of Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential Open
Description of variants found in the NF54 assembly. Excel spreadsheet listing SNP and indel differences found in the NF54 assembly and 3D7.
View article: Additional file 1. of Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential
Additional file 1. of Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential Open
Samples used for analyses in the manuscript “Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential”. Excel spreadsheet listing all samples used in this analysis;…
View article: Additional file 4. of Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential
Additional file 4. of Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential Open
Description of var exon 1 sequences. Excel spreadsheet describing var exon 1 sequences recovered from each of the four PfSPZ strains.
View article: TwinBLAST: When Two Is Better than One
TwinBLAST: When Two Is Better than One Open
Analysis of sequence read pairs can be essential for characterizing structural variation, including junction-spanning pairs of reads (JSPRs) suggesting recent lateral/horizontal gene transfer. TwinBLAST can be used to facilitate this analy…
View article: Strains used in whole organism<i>Plasmodium falciparum</i>vaccine trials differ in genome structure, sequence, and immunogenic potential
Strains used in whole organism<i>Plasmodium falciparum</i>vaccine trials differ in genome structure, sequence, and immunogenic potential Open
Background Plasmodium falciparum (Pf) whole-organism sporozoite vaccines have provided excellent protection against controlled human malaria infection (CHMI) and naturally transmitted heterogeneous Pf in the field. Initial CHMI studies sho…
View article: VIRGO, a comprehensive non-redundant gene catalog, reveals extensive within community intraspecies diversity in the human vagina
VIRGO, a comprehensive non-redundant gene catalog, reveals extensive within community intraspecies diversity in the human vagina Open
Background Analysis of metagenomic and metatranscriptomic data is complicated and typically requires extensive computational resources. Leveraging a curated reference database of genes encoded by members of the target microbiome can make t…
View article: Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project
Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project Open
View article: Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium
Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium Open
View article: Strains, functions and dynamics in the expanded Human Microbiome Project
Strains, functions and dynamics in the expanded Human Microbiome Project Open
The characterization of baseline microbial and functional diversity in the human microbiome has enabled studies of microbiome-related disease, diversity, biogeography, and molecular function. The National Institutes of Health Human Microbi…
View article: CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline
CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline Open
View article: Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data
Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data Open