Noah Spies
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View article: A longitudinal single-cell therapeutic atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease
A longitudinal single-cell therapeutic atlas of anti-tumour necrosis factor treatment in inflammatory bowel disease Open
Precision medicine in immune-mediated inflammatory diseases (IMIDs) requires an understanding of how cellular networks change following therapy. We describe a therapeutic atlas for Crohn’s disease (CD) and ulcerative colitis (UC) following…
View article: SINGLE CELL RNA SEQUENCING OF ULCERATIVE COLITIS AND CROHN'S DISEASE TISSUE SAMPLES INFORMS THE SELECTION OF TREM1 AS A TARGET FOR THE TREATMENT OF INFLAMMATORY BOWEL DISEASES
SINGLE CELL RNA SEQUENCING OF ULCERATIVE COLITIS AND CROHN'S DISEASE TISSUE SAMPLES INFORMS THE SELECTION OF TREM1 AS A TARGET FOR THE TREATMENT OF INFLAMMATORY BOWEL DISEASES Open
Ulcerative colitis (UC) and Crohn’s disease (CD) are complex and heterogenous diseases characterized by chronic and progressive inflammation of the digestive tract. Single cell RNA sequencing combined with computational biology provides un…
View article: A crowdsourced set of curated structural variants for the human genome
A crowdsourced set of curated structural variants for the human genome Open
A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs…
View article: A robust benchmark for germline structural variant detection
A robust benchmark for germline structural variant detection Open
New technologies and analysis methods are enabling genomic structural variants (SVs) to be detected with ever-increasing accuracy, resolution, and comprehensiveness. Translating these methods to routine research and clinical practice requi…
View article: SVCurator: A Crowdsourcing app to visualize evidence of structural variants for the human genome
SVCurator: A Crowdsourcing app to visualize evidence of structural variants for the human genome Open
A high quality benchmark for small variants encompassing 88 to 90% of the reference genome has been developed for seven Genome in a Bottle (GIAB) reference samples. However a reliable benchmark for large indels and structural variants (SVs…
View article: Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2 Open
HepG2 is one of the most widely used human cancer cell lines in biomedical research and one of the main cell lines of ENCODE. Although the functional genomic and epigenomic characteristics of HepG2 are extensively studied, its genome seque…
View article: Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562 Open
K562 is widely used in biomedical research. It is one of three tier-one cell lines of ENCODE and also most commonly used for large-scale CRISPR/Cas9 screens. Although its functional genomic and epigenomic characteristics have been extensiv…
View article: Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2
Haplotype-resolved and integrated genome analysis of the cancer cell line HepG2 Open
SUMMARY The HepG2 cancer cell line is one of the most widely-used biomedical research and one of the main cell lines of ENCODE. Vast numbers of functional genomics and epigenomics datasets have been produced to characterize its biology. Ho…
View article: genomeview - an extensible python-based genomics visualization engine
genomeview - an extensible python-based genomics visualization engine Open
Visual inspection and analysis is integral to quality control, hypothesis generation, methods development and validation of genomic data. The richness and complexity of genomic data necessitates customized visualizations highlighting speci…
View article: Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562
Comprehensive, integrated, and phased whole-genome analysis of the primary ENCODE cell line K562 Open
K562 is widely used in biomedical research. It is one of three tier-one cell lines of ENCODE and also most commonly used for large-scale CRISPR/Cas9 screens. Although its functional genomic and epigenomic characteristics have been extensiv…
View article: Genome-wide reconstruction of complex structural variants using read clouds
Genome-wide reconstruction of complex structural variants using read clouds Open
Recently developed methods that utilize partitioning of long genomic DNA fragments, and barcoding of shorter fragments derived from them, have succeeded in retaining long-range information in short sequencing reads. These so-called read cl…
View article: svclassify: a method to establish benchmark structural variant calls
svclassify: a method to establish benchmark structural variant calls Open
We find that candidate SVs with high scores from multiple technologies have high concordance with PCR validation and an orthogonal consensus method MetaSV (99.7 % concordant), and candidate SVs with low scores are questionable. We distribu…
View article: Additional file 1: Table S1. of svclassify: a method to establish benchmark structural variant calls
Additional file 1: Table S1. of svclassify: a method to establish benchmark structural variant calls Open
Annotations for each of the SV calls as well as likely non-SV regions from the Platinum Genomes 2x100bps HiSeq aligned sequence dataset for NA12878 using svclassify. (CSV 4 kb)
View article: Additional file 12: Table S7. of svclassify: a method to establish benchmark structural variant calls
Additional file 12: Table S7. of svclassify: a method to establish benchmark structural variant calls Open
Manual inspection characteristics of the 20 randomly selected Personalis sites with Ď â >â 0.99 of one-class results. (XLSX 36 kb)
View article: Additional file 4: Table S4. of svclassify: a method to establish benchmark structural variant calls
Additional file 4: Table S4. of svclassify: a method to establish benchmark structural variant calls Open
Annotations for each of the SV calls as well as likely non-SV regions from the PacBio aligned sequence dataset for NA12878 using svclassify. (CSV 1.88 kb)
View article: Additional file 9: Figure S4. of svclassify: a method to establish benchmark structural variant calls
Additional file 9: Figure S4. of svclassify: a method to establish benchmark structural variant calls Open
ROC curves for One-class classification using SVM, treating the 4000 random regions as negatives and the Spiral Genetics insertions calls as positives. (A) ROC curves for one-class models for each dataset separately and for all combined. (…
View article: Additional file 18: Table S13. of svclassify: a method to establish benchmark structural variant calls
Additional file 18: Table S13. of svclassify: a method to establish benchmark structural variant calls Open
Manual inspection characteristics of the 7 randomly selected 1000 Genomes sites with Ď â
View article: Additional file 13: Table S8. of svclassify: a method to establish benchmark structural variant calls
Additional file 13: Table S8. of svclassify: a method to establish benchmark structural variant calls Open
Manual inspection characteristics of all 10 of the randomly selected Personalis sites with 0.9
View article: Additional file 16: Table S11. of svclassify: a method to establish benchmark structural variant calls
Additional file 16: Table S11. of svclassify: a method to establish benchmark structural variant calls Open
Manual inspection characteristics of the 9 randomly selected 1000 Genomes sites with 0.9
View article: Additional file 17: Table S12. of svclassify: a method to establish benchmark structural variant calls
Additional file 17: Table S12. of svclassify: a method to establish benchmark structural variant calls Open
Manual inspection characteristics of the 8 randomly selected 1000 Genomes sites with 0.7
View article: Additional file 15: Table S10. of svclassify: a method to establish benchmark structural variant calls
Additional file 15: Table S10. of svclassify: a method to establish benchmark structural variant calls Open
Manual inspection characteristics of the 20 randomly selected 1000 Genomes sites with Ď â >â 0.99 of one-class results. (XLSX 35 kb)
View article: Additional file 14: Table S9. of svclassify: a method to establish benchmark structural variant calls
Additional file 14: Table S9. of svclassify: a method to establish benchmark structural variant calls Open
Manual inspection characteristics of all 8 of the randomly selected Personalis sites with Ď â
View article: Additional file 3: Table S3. of svclassify: a method to establish benchmark structural variant calls
Additional file 3: Table S3. of svclassify: a method to establish benchmark structural variant calls Open
Annotations for each of the SV calls as well as likely non-SV regions from the Moleculo aligned sequence dataset for NA12878 using svclassify. (CSV 3.02 kb)
View article: Additional file 19: Table S14. of svclassify: a method to establish benchmark structural variant calls
Additional file 19: Table S14. of svclassify: a method to establish benchmark structural variant calls Open
Manual inspection characteristics of the insertions from Spiral Genetics using svviz. (XLSX 118 kb)
View article: Additional file 2: Table S2. of svclassify: a method to establish benchmark structural variant calls
Additional file 2: Table S2. of svclassify: a method to establish benchmark structural variant calls Open
Annotations for each of the SV calls as well as likely non-SV regions from the Illumina HiSeq (read lengthâ =â 250Â bps) aligned sequence dataset for NA12878 using svclassify. (CSV 4 kb)