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Integrative analysis of genomic and transcriptomic data informs precancer progression in the pancreas Open
Pancreatic ductal adenocarcinoma (PDAC) arises from heterogeneous precursor lesions, including intraductal papillary mucinous neoplasms (IPMNs), but the features distinguishing indolent from progressive lesions remain unclear. We performed…
Modeling the involution of microwave liver ablation zones Open
Microwave ablation zones rapidly involute and stabilize at approximately one-third of their baseline volume within a year. The involution process is best modeled by mono-exponential decay and influenced by the type of tissue ablated. These…
Sex‐dimorphic gene regulation in murine macrophages across niches Open
Macrophages are a key cell type of the innate immune system and are involved at all steps of inflammation: (i) they present antigens to initiate inflammation, (ii) they clear up foreign bodies through phagocytosis and (iii) they resolve in…
Balancing ethical data sharing and open science for reproducible research in biomedical data science Open
Analyses of large-scale health data in biomedical data science can help uncover new treatments and deepen our understanding of disease and fundamental biology. Here we examine the balance between ethical and responsible data sharing and op…
Sex-dimorphic gene regulation in murine macrophages across niches Open
Macrophages are a key cell type of the innate immune system and are involved at all steps of inflammation: (i) they present antigens to initiate inflammation, (ii) they clear up foreign bodies through phagocytosis, and (iii) they resolve i…
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 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: Making Common Fund data more findable: catalyzing a data ecosystem
Making Common Fund data more findable: catalyzing a data ecosystem Open
The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables researchers to discover datasets from across the US National Institutes of Health Common Fund without requiring that data owners move, refo…
View article: Making Common Fund data more findable: Catalyzing a Data Ecosystem
Making Common Fund data more findable: Catalyzing a Data Ecosystem Open
The Common Fund Data Ecosystem (CFDE) has created a flexible system of data federation that enables users to discover datasets from across the U.S. National Institutes of Health Common Fund without requiring that data owners move, reformat…
A transcriptomic and epigenomic cell atlas of the mouse primary motor cortex Open
Single-cell transcriptomics can provide quantitative molecular signatures for large, unbiased samples of the diverse cell types in the brain 1–3 . With the proliferation of multi-omics datasets, a major challenge is to validate and integra…
Two Year Progression of Working Memory Impairments In Early Relapsing-Remitting Multiple Sclerosis: Appraisal of Working Memory Profiles And Measurement Sensitivity Open
Working memory (WMem) impairments are a devastating symptom of Multiple Sclerosis (MS) that manifest as distinct profiles depending upon the type of impairment. It is unknown what WMem impairment profiles occur in early MS and how best to …
Learning Lessons for Evaluating Complexity Across the Nexus: A Meta-Evaluation of Environmental Projects Open
Background: A major gap in environmental policy making is learning lessons from past interventions and in integrating the lessons from evaluations that have been undertaken. Institutional memory of such evaluations often resides externally…
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, var…
Human microbiome science: vision for the future, Bethesda, MD, July 24 to 26, 2013 Open
A conference entitled ‘Human microbiome science: Vision for the future’ was organized in Bethesda, MD from July 24 to 26, 2013. The event brought together experts in the field of human microbiome research and aimed at providing a comprehen…
View article: Toward unrestricted use of public genomic data
Toward unrestricted use of public genomic data Open
Publication interests should not limit access to public data
Characterisation of the attenuation properties of 3D-printed tungsten for use in gamma camera collimation Open
SLM manufacture of tungsten collimators is feasible. Attenuation properties of SLM tungsten are superior to the lead alternative and the opportunity for bespoke collimator design is appealing.
2019-July_CFDE_AssessmentReport.pdf Open
July 2019 Assessment Report for the Common Fund Data Ecosystem.
Additional file 2: Table S2. of CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline Open
Example of a summary report from the comparative analysis of 40 E. coli genomes as listed in Table 1. (TXT 3 kb)
Additional file 1: Table S1. of CloVR-Comparative: automated, cloud-enabled comparative microbial genome sequence analysis pipeline Open
List of components and scripts used by CloVR-Comparative, including links to corresponding software repositories. (TXT 2 kb)