J Christopher Bare
YOU?
Author Swipe
View article: Profiling lamina specific pyramidal neurons using postmortem human formalin fixed paraffin embedded frontal cortex tissue in combination with digital spatial profiling
Profiling lamina specific pyramidal neurons using postmortem human formalin fixed paraffin embedded frontal cortex tissue in combination with digital spatial profiling Open
This optimized DSP assay provides high resolution RNA-seq data demonstrating utility and versatility of the GeoMx platform for individually characterized neurons and isolated cortical ribbons within postmortem FFPE human brain tissue for d…
View article: Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection Open
View article: Germline contamination and leakage in whole genome somatic single nucleotide variant detection
Germline contamination and leakage in whole genome somatic single nucleotide variant detection Open
The potential for patient re-identification from leaked germline variants in somatic SNV predictions has led to divergent open data access policies, based on different assessments of the risks. Indeed, a single, well-publicized re-identifi…
View article: Additional file 2: Table S2. of Germline contamination and leakage in whole genome somatic single nucleotide variant detection
Additional file 2: Table S2. of Germline contamination and leakage in whole genome somatic single nucleotide variant detection Open
Contains the following information for every challenge submission: tumour, submission ID, precision, recall, F1-score, the number of germline variants leaked and whether it was a Challenge administrator submission. (XLS 39Â kb)
View article: Additional file 7: of Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
Additional file 7: of Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection Open
BAMSurgeon input files used to generate the three in silico tumor-normal pairs (IS1-IS3). (GZ 122 kb)
View article: Additional file 3: of Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
Additional file 3: of Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection Open
Table S2. All competition-phase submissions evaluated with fâ =â 100 and jâ >â 0. (XLS 43 kb)
View article: Additional file 1: Table S1. of Germline contamination and leakage in whole genome somatic single nucleotide variant detection
Additional file 1: Table S1. of Germline contamination and leakage in whole genome somatic single nucleotide variant detection Open
Tumour information from each tumour challenge (IS1, IS2, IS3). This includes information on in silico tumour construction, composition, and a summary of participating teams and their challenge submissions. (XLS 12Â kb)
View article: Additional file 6: of Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
Additional file 6: of Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection Open
Table S4. Univariate error analysis. (XLS 13 kb)
View article: Additional file 2: of Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
Additional file 2: of Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection Open
Table S1. Challenge participation. (XLS 5 kb)
View article: Additional file 5: of Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection
Additional file 5: of Combining accurate tumor genome simulation with crowdsourcing to benchmark somatic structural variant detection Open
Table S3. Invalid SV types. (XLS 7 kb)
View article: Prediction of Human Population Responses to Toxic Compounds by a Collaborative Competition
Prediction of Human Population Responses to Toxic Compounds by a Collaborative Competition Open
When it becomes completely possible for one to computationally forecast the impacts of harmful substances on humans, it would be easier to attempt addressing the shortcomings of existing safety testing for chemicals. In this paper, we rela…
View article: Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic structural variant detection
Combining accurate tumour genome simulation with crowd-sourcing to benchmark somatic structural variant detection Open
Background The phenotypes of cancer cells are driven in part by somatic structural variants. Structural variants can initiate tumors, enhance their aggressiveness and provide unique therapeutic opportunities. Whole-genome sequencing of tum…
View article: Germline Contamination and Leakage in Whole Genome Somatic Single Nucleotide Variant Detection
Germline Contamination and Leakage in Whole Genome Somatic Single Nucleotide Variant Detection Open
Background The clinical sequencing of cancer genomes to personalize therapy is becoming routine across the world. However, concerns over patient re-identification from these data lead to questions about how tightly access should be control…
View article: Evaluating the Knowledge Base and Current Training of Paramedics in the Southwest United States in Assessing and Managing Toxic Alcohol Exposures
Evaluating the Knowledge Base and Current Training of Paramedics in the Southwest United States in Assessing and Managing Toxic Alcohol Exposures Open
Introduction Toxic alcohol overdose poses a problem in patients who are suffering from the toxicological consequences of toxic alcohol exposure and front line emergency care providers, such as paramedics, need to be well versed in assessin…
View article: Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data
Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data Open
View article: Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease
Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease Open
Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimer's disease. The Alzheimer's disease DREAM Challenge was designed as a computational crowdsourced project t…
View article: dreamtools: Release synchronised with F1000 second version.
dreamtools: Release synchronised with F1000 second version. Open
Code sharing related to DREAM challenges
View article: The mPower study, Parkinson disease mobile data collected using ResearchKit
The mPower study, Parkinson disease mobile data collected using ResearchKit Open
View article: dreamtools: Tag for a conda release
dreamtools: Tag for a conda release Open
Code sharing related to DREAM challenges
View article: Erratum: Prediction of human population responses to toxic compounds by a collaborative competition
Erratum: Prediction of human population responses to toxic compounds by a collaborative competition Open
View article: Prediction of human population responses to toxic compounds by a collaborative competition
Prediction of human population responses to toxic compounds by a collaborative competition Open
View article: Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection
Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection Open