List of works by Jonathan Crabtree

A Prototype Platform for Policy-Based Archive Replication

article by Micah Altman et al published 1 November 2013 in Against the Grain

A catalog of reference genomes from the human microbiome

scientific article

A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina

scientific article published on 26 February 2020

A data analysis and coordination center for the human microbiome project.

scientific article

A multimodal cell census and atlas of the mammalian primary motor cortex

scientific article

A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex

scientific article

An integrated genomic and transcriptomic survey of mucormycosis-causing fungi

scientific article published on 22 July 2016

ApiEST-DB: analyzing clustered EST data of the apicomplexan parasites

scientific article

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium.

scientific article

Capture-based enrichment of Theileria parva DNA enables full genome assembly of first buffalo-derived strain and reveals exceptional intra-specific genetic diversity

scientific article published on 29 October 2020

Circleator: flexible circular visualization of genome-associated data with BioPerl and SVG.

scientific article

CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline

scientific article

Comparative genomics of Brassica oleracea and Arabidopsis thaliana reveal gene loss, fragmentation, and dispersal after polyploidy

article

Comparative genomics of emerging human ehrlichiosis agents

scientific article

Comparative genomics of mutualistic viruses of Glyptapanteles parasitic wasps

scientific article published on 30 December 2008

Comparative genomics of the neglected human malaria parasite Plasmodium vivax

scientific article

Comparative genomics of trypanosomatid parasitic protozoa

scientific article (publication date: 15 July 2005)

Computational Methods and Bioinformatic Tools

Continuing evolution of Burkholderia mallei through genome reduction and large-scale rearrangements

scientific article

Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents.

scientific article

Digital Preservation through Archival Collaboration: The Data Preservation Alliance for the Social Sciences

Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data

scientific article

Draft Genome Sequences of Human Pathogenic Fungus Geomyces pannorum Sensu Lato and Bat White Nose Syndrome Pathogen Geomyces (Pseudogymnoascus) destructans

scientific article published on 19 December 2013

Draft genome of the filarial nematode parasite Brugia malayi

scientific article

Draft genome sequence of the oilseed species Ricinus communis

scientific article

Ergatis: a web interface and scalable software system for bioinformatics workflows

scientific article

Erratum: Strains, functions and dynamics in the expanded Human Microbiome Project

scientific article published on 12 October 2017

From Preserving the Past to Preserving the Future: The Data-PASS Project and the Challenges of Preserving Digital Social Science Data

Functional dynamics of the gut microbiome in elderly people during probiotic consumption

scientific article published on 14 April 2015

Genome Sequence of Theileria parva, a Bovine Pathogen That Transforms Lymphocytes

scientific article

Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome"

scientific article

Genome sequence of Aedes aegypti, a major arbovirus vector

scientific article

Genome sequence of Babesia bovis and comparative analysis of apicomplexan hemoprotozoa

scientific article published on 19 October 2007

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions

scientific article published on 18 October 2016

Genomic epidemiology of the Haitian cholera outbreak: a single introduction followed by rapid, extensive, and continued spread characterized the onset of the epidemic.

scientific article

Genomic islands in the pathogenic filamentous fungus Aspergillus fumigatus

scientific article

Global Phylogeny of Mycobacterium tuberculosis Based on Single Nucleotide Polymorphism (SNP) Analysis: Insights into Tuberculosis Evolution, Phylogenetic Accuracy of Other DNA Fingerprinting Systems, and Recommendations for a Minimal Standard SNP Set

scholarly article by Ingrid Filliol et al published 3 April 2006 in Journal of Bacteriology

Global phylogeny of Mycobacterium tuberculosis based on single nucleotide polymorphism (SNP) analysis: insights into tuberculosis evolution, phylogenetic accuracy of other DNA fingerprinting systems, and recommendations for a minimal standard SNP se

scientific article

HMPDACC: a Human Microbiome Project Multi-omic data resource

scientific article published on 10 December 2020

IDEA: Interactive Display for Evolutionary Analyses

scientific article

Interactive exploratory data analysis of Integrative Human Microbiome Project data using Metaviz

scientific article published on 12 June 2020

New resources for functional analysis of omics data for the genus Aspergillus

scientific article

PlasmoDB: the Plasmodium genome resource. A database integrating experimental and computational data

scientific article

PlasmoDB: the Plasmodium genome resource. An integrated database providing tools for accessing, analyzing and mapping expression and sequence data (both finished and unfinished).

scientific article

Strains used in whole organism Plasmodium falciparum vaccine trials differ in genome structure, sequence, and immunogenic potential

scientific article published on 08 January 2020

Strains, functions and dynamics in the expanded Human Microbiome Project

scientific article

Sub-telomere directed gene expression during initiation of invasive aspergillosis

scientific article

Sybil: methods and software for multiple genome comparison and visualization

scientific article

The Aspergillus Genome Database (AspGD): recent developments in comprehensive multispecies curation, comparative genomics and community resources

scientific article published on 12 November 2011

The Aspergillus Genome Database, a curated comparative genomics resource for gene, protein and sequence information for the Aspergillus research community

scientific article

The Genome Sequence of Trypanosoma cruzi, Etiologic Agent of Chagas Disease

scientific article

The HuRef Browser: a web resource for individual human genomics

scientific article published on 26 November 2008

The Plasmodium genome database

scientific article published in Nature

The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates

scientific article published in August 2008

Transcriptional program of the endocrine pancreas in mice and humans.

scientific article

TwinBLAST: When Two Is Better than One

scientific article published on 29 August 2019

Using Sybil for interactive comparative genomics of microbes on the web.

scientific article

Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition

scientific article

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