Joshua Orvis
YOU?
Author Swipe
View article: A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development
A Curated Compendium of Transcriptomic Data for the Exploration of Neocortical Development Open
Vast quantities of multi-omic data have been produced to characterize the development and diversity of cell types in the cerebral cortex of humans and other mammals. To more fully harness the collective discovery potential of these data, w…
View article: A guide to the BRAIN Initiative Cell Census Network data ecosystem
A guide to the BRAIN Initiative Cell Census Network data ecosystem Open
Characterizing cellular diversity at different levels of biological organization and across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also essential to manipula…
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 BRAIN Initiative Cell Census Network Data Ecosystem: A User’s Guide
The BRAIN Initiative Cell Census Network Data Ecosystem: A User’s Guide Open
Characterizing cellular diversity at different levels of biological organization across data modalities is a prerequisite to understanding the function of cell types in the brain. Classification of neurons is also required to manipulate ce…
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 evolution of synaptic and cognitive capacity: Insights from the nervous system transcriptome of<i>Aplysia</i>
The evolution of synaptic and cognitive capacity: Insights from the nervous system transcriptome of<i>Aplysia</i> Open
The gastropod mollusk Aplysia is an important model for cellular and molecular neurobiological studies, particularly for investigations of molecular mechanisms of learning and memory. We developed an optimized assembly pipeline to generate…
View article: Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse
Author Correction: Comparative cellular analysis of motor cortex in human, marmoset and mouse Open
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: Comparative cellular analysis of motor cortex in human, marmoset and mouse
Comparative cellular analysis of motor cortex in human, marmoset and mouse Open
View article: A cell-type-specific atlas of the inner ear transcriptional response to acoustic trauma
A cell-type-specific atlas of the inner ear transcriptional response to acoustic trauma Open
Noise-induced hearing loss (NIHL) results from a complex interplay of damage to the sensory cells of the inner ear, dysfunction of its lateral wall, axonal retraction of type 1C spiral ganglion neurons, and activation of the immune respons…
View article: Regulation and Autoregulation of the Promoter for the Latency-associated Nuclear Antigen of Kaposi's Sarcoma-associated Herpesvirus
Regulation and Autoregulation of the Promoter for the Latency-associated Nuclear Antigen of Kaposi's Sarcoma-associated Herpesvirus Open
Kaposi's sarcoma-associated herpesvirus (KSHV) or human herpesvirus 8 has been established as the etiological agent of Kaposi's sarcoma and certain AIDS-associated lymphomas. KSHV establishes latent infection in these tumors, invariably ex…
View article: gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration
gEAR: Gene Expression Analysis Resource portal for community-driven, multi-omic data exploration Open
View article: NeMO analytics‐AD: The neuroscience multi‐omic visualization and analysis platform, now extended to support Alzheimer’s disease
NeMO analytics‐AD: The neuroscience multi‐omic visualization and analysis platform, now extended to support Alzheimer’s disease Open
Background Recent years have resulted in tremendous progress in understanding Alzheimer’s disease via the generation and analysis of multi‐omic data. In addition, the BRAIN initiative has been mapping gene expression in the normal brain, w…
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: gEAR: gene Expression Analysis Resource portal for community-driven, multi-omic data exploration
gEAR: gene Expression Analysis Resource portal for community-driven, multi-omic data exploration Open
The gEAR portal (gene Expression Analysis Resource, umgear.org) is an open access community-driven tool for multi-omic and multi-species data visualization, analysis and sharing. The gEAR supports visualization of multiple RNA-seq data typ…
View article: Characterization of the development of the mouse cochlear epithelium at the single cell level
Characterization of the development of the mouse cochlear epithelium at the single cell level Open
Mammalian hearing requires the development of the organ of Corti, a sensory epithelium comprising unique cell types. The limited number of each of these cell types, combined with their close proximity, has prevented characterization of ind…
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: Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms
Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms Open
View article: Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse
Evolution of cellular diversity in primary motor cortex of human, marmoset monkey, and mouse Open
The primary motor cortex (M1) is essential for voluntary fine motor control and is functionally conserved across mammals. Using high-throughput transcriptomic and epigenomic profiling of over 450,000 single nuclei in human, marmoset monkey…
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: Additional file 2 of Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms
Additional file 2 of Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms Open
Additional file 2. Pairs of consecutive genes with overlap in UTR only or both UTR and CDS.
View article: Additional file 3 of Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms
Additional file 3 of Re-annotation of the Theileria parva genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms Open
Additional file 3. Ratio of intron_coverage by average_CDS_coverage, for introns with read_coverage> 0.
View article: Re-annotation of the <i>Theileria parva</i> genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms
Re-annotation of the <i>Theileria parva</i> genome refines 53% of the proteome and uncovers essential components of N-glycosylation, a conserved pathway in many organisms Open
Background The apicomplexan parasite Theileria parva causes a livestock disease called East coast fever (ECF), with millions of animals are at risk in sub-Saharan East and Southern Africa, the geographic distribution of T. parva . Over a m…
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: 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: Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions
Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions Open
View article: Annotated draft genome sequences of three species of<i>Cryptosporidium</i>:<i>Cryptosporidium meleagridis</i>isolate UKMEL1,<i>C. baileyi</i>isolate TAMU-09Q1 and<i>C. hominis</i>isolates TU502_2012 and UKH1
Annotated draft genome sequences of three species of<i>Cryptosporidium</i>:<i>Cryptosporidium meleagridis</i>isolate UKMEL1,<i>C. baileyi</i>isolate TAMU-09Q1 and<i>C. hominis</i>isolates TU502_2012 and UKH1 Open
Human cryptosporidiosis is caused primarily by Cryptosporidium hominis, C. parvum and C. meleagridis. To accelerate research on parasites in the genus Cryptosporidium, we generated annotated, draft genome sequences of human C. hominis isol…
View article: An integrated genomic and transcriptomic survey of mucormycosis-causing fungi
An integrated genomic and transcriptomic survey of mucormycosis-causing fungi Open
View article: The genome sequence of four isolates from the family Lichtheimiaceae
The genome sequence of four isolates from the family Lichtheimiaceae Open
This study reports the release of draft genome sequences of two isolates of Lichtheimia corymbifera and two isolates of L. ramosa. Phylogenetic analyses indicate that the two L. corymbifera strains (CDC-B2541 and 008-049) are closely relat…