Nicolas Bray
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View article: FIREBall-2 UV balloon telescope in-flight calibration system
FIREBall-2 UV balloon telescope in-flight calibration system Open
International audience
View article: The impact of package selection and versioning on single-cell RNA-seq analysis
The impact of package selection and versioning on single-cell RNA-seq analysis Open
Summary Standard single-cell RNA-sequencing analysis (scRNA-seq) workflows consist of converting raw read data into cell-gene count matrices through sequence alignment, followed by analyses including filtering, highly variable gene selecti…
View article: kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq
kallisto, bustools, and kb-python for quantifying bulk, single-cell, and single-nucleus RNA-seq Open
The term “RNA-seq” refers to a collection of assays based on sequencing experiments that involve quantifying RNA species from bulk tissue, from single cells, or from single nuclei. The kallisto, bustools, and kb-python programs are free, o…
View article: Voyager: exploratory single-cell genomics data analysis with geospatial statistics
Voyager: exploratory single-cell genomics data analysis with geospatial statistics Open
Exploratory spatial data analysis (ESDA) can be a powerful approach to understanding single-cell genomics datasets, but it is not yet part of standard data analysis workflows. In particular, geospatial analyses, which have been developed a…
View article: FIREBall-2: flight preparation of a proven balloon payload to image the\n intermediate redshift circumgalactic medium
FIREBall-2: flight preparation of a proven balloon payload to image the\n intermediate redshift circumgalactic medium Open
FIREBall-2 is a stratospheric balloon-borne 1-m telescope coupled to a UV\nmulti-object slit spectrograph designed to map the faint UV emission\nsurrounding z~0.7 galaxies and quasars through their Lyman-alpha line emission.\nThis spectro-…
View article: FIREBall-2: flight preparation of a proven balloon payload to image the intermediate redshift circumgalactic medium
FIREBall-2: flight preparation of a proven balloon payload to image the intermediate redshift circumgalactic medium Open
FIREBall-2 is a stratospheric balloon-borne 1-m telescope coupled to a UV multi-object slit spectrograph designed to map the faint UV emission surrounding z~0.7 galaxies and quasars through their Lyman-alpha line emission. This spectro-ima…
View article: End-to-end ground calibration and in-flight performance of the\n FIREBall-2 instrument
End-to-end ground calibration and in-flight performance of the\n FIREBall-2 instrument Open
The payload of the Faint Intergalactic Redshifted Emission Balloon\n(FIREBall-2), the second generation of the FIREBall instrument (PI: C. Martin,\nCaltech), has been calibrated and launched from the NASA Columbia Scientific\nBalloon Facil…
View article: Controlled Cycling and Quiescence Enables Efficient HDR in Engraftment-Enriched Adult Hematopoietic Stem and Progenitor Cells
Controlled Cycling and Quiescence Enables Efficient HDR in Engraftment-Enriched Adult Hematopoietic Stem and Progenitor Cells Open
Genome editing often takes the form of either error-prone sequence disruption by non-homologous end joining (NHEJ) or sequence replacement by homology-directed repair (HDR). Although NHEJ is generally effective, HDR is often difficult in p…
View article: FIREBall-2: advancing TRL while doing proof-of-concept astrophysics on a\n suborbital platform
FIREBall-2: advancing TRL while doing proof-of-concept astrophysics on a\n suborbital platform Open
Here we discuss advances in UV technology over the last decade, with an\nemphasis on photon counting, low noise, high efficiency detectors in\nsub-orbital programs. We focus on the use of innovative UV detectors in a NASA\nastrophysics bal…
View article: Expression reflects population structure
Expression reflects population structure Open
Population structure in genotype data has been extensively studied, and is revealed by looking at the principal components of the genotype matrix. However, no similar analysis of population structure in gene expression data has been conduc…
View article: Expression reflects population structure
Expression reflects population structure Open
Population structure in genotype data has been extensively studied, and is revealed by looking at the principal components of the genotype matrix. However, no similar analysis of population structure in gene expression data has been conduc…
View article: Controlled cycling and quiescence enables homology directed repair in engraftment-enriched adult hematopoietic stem and progenitor cells
Controlled cycling and quiescence enables homology directed repair in engraftment-enriched adult hematopoietic stem and progenitor cells Open
Summary Hematopoietic stem cells (HSCs) are the source of all blood components, and genetic defects in these cells are causative of disorders ranging from severe combined immunodeficiency to sickle cell disease. However, genome editing of …
View article: Gene-level differential analysis at transcript-level resolution
Gene-level differential analysis at transcript-level resolution Open
Compared to RNA-sequencing transcript differential analysis, gene-level differential expression analysis is more robust and experimentally actionable. However, the use of gene counts for statistical analysis can mask transcript-level dynam…
View article: kallisto quantifications of Frahm et al., 2017
kallisto quantifications of Frahm et al., 2017 Open
The analysis was performed in Yi et al., 2017, which used p-value aggregation on transcript differential analysis to make gene-level determinations. For more details, see https://doi.org/10.1186/s13059-018-1419-zWe analyzed a dataset (GEO …
View article: kallisto quantifications of Frahm et al., 2017
kallisto quantifications of Frahm et al., 2017 Open
The analysis was performed in Yi et al., 2017, which used p-value aggregation on transcript differential analysis to make gene-level determinations. For more details, see https://doi.org/10.1186/s13059-018-1419-zWe analyzed a dataset (GEO …
View article: Gene-level differential analysis at transcript-level resolution
Gene-level differential analysis at transcript-level resolution Open
Gene-level differential expression analysis based on RNA-Seq is more robust, powerful and biologically actionable than transcript-level differential analysis. However aggregation of transcript counts prior to analysis results can mask tran…
View article: Fusion detection and quantification by pseudoalignment
Fusion detection and quantification by pseudoalignment Open
RNA sequencing in cancer cells is a powerful technique to detect chromosomal rearrangements, allowing for de novo discovery of actively expressed fusion genes. Here we focus on the problem of detecting gene fusions from raw sequencing data…
View article: Disabling Cas9 by an anti-CRISPR DNA mimic
Disabling Cas9 by an anti-CRISPR DNA mimic Open
Natural inhibitors of Cas9 pretend to be DNA and block target binding, and using them in human cells can reduce off-target events.
View article: Pseudoalignment for metagenomic read assignment
Pseudoalignment for metagenomic read assignment Open
Motivation Read assignment is an important first step in many metagenomic analysis workflows, providing the basis for identification and quantification of species. However ambiguity among the sequences of many strains makes it difficult to…
View article: Discovery of an autoimmunity-associated <i>IL2RA</i> enhancer by unbiased targeting of transcriptional activation
Discovery of an autoimmunity-associated <i>IL2RA</i> enhancer by unbiased targeting of transcriptional activation Open
The majority of genetic variants associated with common human diseases map to enhancers, non-coding elements that shape cell type-specific transcriptional programs and responses to specific extracellular cues 1-3 . In order to understand t…
View article: Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells
Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells Open
Hematopoietic stem cells from patients with sickle cell disease can be edited by CRISPR/Cas9 and maintain the edits in vivo.
View article: The Lair: A resource for exploratory analysis of published RNA-Seq data
The Lair: A resource for exploratory analysis of published RNA-Seq data Open
Increased emphasis on reproducibility of published research in the last few years has led to the large-scale archiving of sequencing data. While this data can, in theory, be used to reproduce results in papers, it is typically not easily u…
View article: Efficient Correction of the Sickle Mutation in Human Hematopoietic Stem Cells Using a Cas9 Ribonucleoprotein Complex
Efficient Correction of the Sickle Mutation in Human Hematopoietic Stem Cells Using a Cas9 Ribonucleoprotein Complex Open
Sickle Cell Disease (SCD) is a serious recessive genetic disorder caused by a single nucleotide polymorphism (SNP) in the ß-globin gene ( HBB ). Sickle hemoglobin polymerizes within red blood cells (RBCs), causing them to adopt an elongate…