Lista de obras - John Marioni - Dominio Público Uruguay

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

artículo científico publicado en 2008

A comparison of dermatologists', surgeons' and general practitioners' surgical management of cutaneous melanoma

artículo científico publicado en 2004

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

artículo científico publicado en 2011

A single-cell molecular map of mouse gastrulation and early organogenesis

scientific article published on 20 February 2019

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

artículo científico publicado en 2016

A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans

scientific article published on 31 July 2019

Accounting for technical noise in single-cell RNA-seq experiments.

artículo científico publicado en 2013

Ageing compromises mouse thymus function and remodels epithelial cell differentiation

artículo científico publicado en 2020

Aging increases cell-to-cell transcriptional variability upon immune stimulation

artículo científico publicado en 2017

Altered composition of the γδ T cell pool in lymph nodes during ageing enhances tumour growth

article

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

artículo científico publicado en 2008

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data ⬇️

artículo científico publicado en 2017

Author Correction: Challenges in measuring and understanding biological noise

artículo científico publicado en 2019

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

artículo científico publicado en 2015

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

artículo científico publicado en 2018

Beyond comparisons of means: understanding changes in gene expression at the single-cell level

artículo científico publicado en 2016

Beyond comparisons of means: understanding changes in gene expression at the single-cell level

article

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

artículo científico publicado en 2007

COMRADES determines in vivo RNA structures and interactions

artículo científico publicado en 2018

CTCF maintains regulatory homeostasis of cancer pathways

scientific article published on 07 August 2018

Cells of the human intestinal tract mapped across space and time

Challenges in measuring and understanding biological noise

artículo científico publicado en 2019

Characterization of a common progenitor pool of the epicardium and myocardium

scientific article published on 07 January 2021

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

artículo científico publicado en 2015

Classification of low quality cells from single-cell RNA-seq data

artículo científico publicado en 2016

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.

artículo científico publicado en 2016

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

artículo científico publicado en 2012

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

artículo científico publicado en 2015

Computational and analytical challenges in single-cell transcriptomics

artículo científico publicado en 2015

Computational assignment of cell-cycle stage from single-cell transcriptome data

artículo científico publicado en 2015

Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone

artículo científico publicado en 2015

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals

artículo científico publicado en 2013

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

artículo científico publicado en 2018

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

artículo científico publicado en 2019

Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

artículo científico publicado en 2016

CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.

artículo científico publicado en 2018

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection

artículo científico publicado en 2012

Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.

artículo científico publicado en 2018

Detection and removal of barcode swapping in single-cell RNA-seq data

scientific article published in Nature Communications

Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing

artículo científico publicado en 2017

Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

ESR1 gene amplification in breast cancer: a common phenomenon?

artículo científico publicado en 2008

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

artículo científico publicado en 2009

Effects of a brief course of azithromycin on soluble cell adhesion molecules and markers of inflammation in survivors of an acute coronary syndrome: A double-blind, randomized, placebo-controlled study

artículo científico publicado en 2004

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

article by Aaron T L Lun et al published 22 March 2019 in Genome Biology

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

artículo científico publicado en 2014

Expression Atlas update: gene and protein expression in multiple species

artículo científico publicado en 2021

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

artículo científico publicado en 2012

Functional comparison of innate immune signaling pathways in primates

artículo científico publicado en 2010

Gene expression differences among primates are associated with changes in a histone epigenetic modification

artículo científico publicado en 2011

Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.

artículo científico publicado en 2014

Genomic-scale capture and sequencing of endogenous DNA from feces

artículo científico publicado en 2010

Guidelines for reporting single-cell RNA-seq experiments

artículo científico publicado en 2020

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.

artículo científico publicado en 2016

Hidden copy number variation in the HapMap population.

artículo científico publicado en 2008

Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq

artículo científico publicado en 2015

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer

artículo científico publicado en 2007

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface

artículo científico publicado en 2014

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

artículo científico publicado en 2015

How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology

artículo científico publicado en 2017

IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response

artículo científico publicado en 2019

Identification of a regeneration-organizing cell in the Xenopus tail

artículo científico publicado en 2019

Identifying cell types from spatially referenced single-cell expression datasets

artículo científico publicado en 2014

Impact of Alternative Splicing on the Human Proteome

artículo científico publicado en 2017

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

artículo científico publicado en 2013

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.

artículo científico publicado en 2017

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.

artículo científico publicado en 2013

Investigating higher-order interactions in single-cell data with scHOT

scientific article published on 13 July 2020

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells

artículo científico publicado en 2017

LifeTime and improving European healthcare through cell-based interceptive medicine

artículo científico publicado en 2020

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis

artículo científico publicado en 2014

Mapping Rora expression in resting and activated CD4+ T cells

artículo científico publicado en 2021

Molecular and neuronal homology between the olfactory systems of zebrafish and mouse

artículo científico publicado en 2015

Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data

artículo científico publicado en 2017

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

artículo científico publicado en 2018

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

artículo científico publicado en 2014

Normalizing single-cell RNA sequencing data: challenges and opportunities

artículo científico publicado en 2017

Numbers of copy-number variations and false-negative rates will be underestimated if we do not account for the dependence between repeated experiments

artículo científico publicado en 2007

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data

artículo científico publicado en 2017

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data

scholarly article published 8 September 2016

Pluripotent state transitions coordinate morphogenesis in mouse and human embryos

artículo científico publicado en 2017

Pooling across cells to normalize single-cell RNA sequencing data with many zero counts.

artículo científico publicado en 2016

Population-scale single-cell RNA-seq profiling across dopaminergic neuron differentiation

artículo científico publicado en 2021

Publisher Correction: LifeTime and improving European healthcare through cell-based interceptive medicine

artículo científico publicado en 2021

Publisher Correction: Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

artículo científico publicado en 2020

Quantitative genetic analysis deciphers the impact of cis and trans regulation on cell-to-cell variability in protein expression levels

artículo científico publicado en 2020

RNA-Seq gene profiling--a systematic empirical comparison

artículo científico publicado en 2014

RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays

artículo científico publicado en 2008

Random monoallelic gene expression increases upon embryonic stem cell differentiation

artículo científico publicado en 2014

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength

artículo científico publicado en 2015

Regulatory Divergence of Transcript Isoforms in a Mammalian Model System

artículo científico publicado en 2015

Resolving early mesoderm diversification through single-cell expression profiling

artículo científico publicado en 2016

Resolving the fibrotic niche of human liver cirrhosis at single-cell level

scientific article published on 09 October 2019

SRPK1 maintains acute myeloid leukemia through effects on isoform usage of epigenetic regulators including BRD4

artículo científico publicado en 2018

SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements.

artículo científico publicado en 2018

Sex-specific and lineage-specific alternative splicing in primates

artículo científico publicado en 2009

Single Cell Genomics meeting in Stockholm: from single cells to cell types

artículo científico publicado en 2014

Single Cell RNA-Sequencing of Pluripotent States Unlocks Modular Transcriptional Variation

artículo científico publicado en 2015

Single-Cell Landscape of Transcriptional Heterogeneity and Cell Fate Decisions during Mouse Early Gastrulation

artículo científico publicado en 2017

Single-cell RNA-sequencing of differentiating iPS cells reveals dynamic genetic effects on gene expression

artículo científico publicado en 2020

Single-cell multi-omics analysis of the immune response in COVID-19

artículo científico publicado en 2021

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

artículo científico publicado en 2018

Specificity of RNAi, LNA and CRISPRi as loss-of-function methods in transcriptional analysis

Staged developmental mapping and X chromosome transcriptional dynamics during mouse spermatogenesis

artículo científico publicado en 2019

Stella modulates transcriptional and endogenous retrovirus programs during maternal-to-zygotic transition.

artículo científico publicado en 2017

Stimulation strength controls the rate of initiation but not the molecular organization of TCR-induced signalling

artículo científico publicado en 2020

Structure and evolutionary history of a large family of NLR proteins in the zebrafish

artículo científico publicado en 2016

Structure and evolutionary history of a large family of NLR proteins in the zebrafish

Support for a clade of Placozoa and Cnidaria in genes with minimal compositional bias

article

T cell cytolytic capacity is independent of initial stimulation strength

scholarly article by Arianne C Richard et al published 16 July 2018 in Nature Immunology

Testing for differential abundance in mass cytometry data

artículo científico publicado en 2017

Testing the mean matrix in high-dimensional transposable data ⬇️

artículo científico publicado en 2015

The Human Cell Atlas

artículo científico publicado en 2017

The Human Cell Atlas White Paper ⬇️

artículo científico publicado en 2018

The T-box transcription factor Eomesodermin governs haemogenic competence of yolk sac mesodermal progenitors

artículo científico publicado en 2021

The cellular immune response to COVID-19 deciphered by single cell multi-omics across three UK centres

artículo científico publicado en 2021

The pitfalls of platform comparison: DNA copy number array technologies assessed

artículo científico publicado en 2009

The technology and biology of single-cell RNA sequencing

artículo científico publicado en 2015

Tools for mapping high-throughput sequencing data

artículo científico publicado en 2012

Toward a Common Coordinate Framework for the Human Body

scientific article published on 01 December 2019

Using single-cell genomics to understand developmental processes and cell fate decisions.

artículo científico publicado en 2018

Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body

artículo científico publicado en 2018

Whole-body single-cell sequencing of the Platynereis larva reveals a subdivision into apical versus non-apical tissues

Yolk sac cell atlas reveals multiorgan functions during human early development

artículo científico publicado en 2023

bioWeb3D: an online webGL 3D data visualisation tool

artículo científico publicado en 2013

f-scLVM: scalable and versatile factor analysis for single-cell RNA-seq.

artículo científico publicado en 2017

scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells

artículo científico publicado en 2018

Lista de obras de John Marioni

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

A comparison of dermatologists', surgeons' and general practitioners' surgical management of cutaneous melanoma

A genome-wide study of DNA methylation patterns and gene expression levels in multiple human and chimpanzee tissues.

A single-cell molecular map of mouse gastrulation and early organogenesis

A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor.

A transcriptomic atlas of mammalian olfactory mucosae reveals an evolutionary influence on food odor detection in humans

Accounting for technical noise in single-cell RNA-seq experiments.

Ageing compromises mouse thymus function and remodels epithelial cell differentiation

Aging increases cell-to-cell transcriptional variability upon immune stimulation

Altered composition of the γδ T cell pool in lymph nodes during ageing enhances tumour growth

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data ⬇️

Author Correction: Challenges in measuring and understanding biological noise

BASiCS: Bayesian Analysis of Single-Cell Sequencing Data

Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors

Beyond comparisons of means: understanding changes in gene expression at the single-cell level

Beyond comparisons of means: understanding changes in gene expression at the single-cell level

Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization.

COMRADES determines in vivo RNA structures and interactions

CTCF maintains regulatory homeostasis of cancer pathways

Cells of the human intestinal tract mapped across space and time

Challenges in measuring and understanding biological noise

Characterization of a common progenitor pool of the epicardium and myocardium

Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

Classification of low quality cells from single-cell RNA-seq data

Codon-Driven Translational Efficiency Is Stable across Diverse Mammalian Cell States.

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells

Computational and analytical challenges in single-cell transcriptomics

Computational assignment of cell-cycle stage from single-cell transcriptome data

Contributions to drug resistance in glioblastoma derived from malignant cells in the sub-ependymal zone

Cooperativity and rapid evolution of cobound transcription factors in closely related mammals

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

Correcting the Mean-Variance Dependency for Differential Variability Testing Using Single-Cell RNA Sequencing Data

Corrigendum: Characterizing noise structure in single-cell RNA-seq distinguishes genuine from technical stochastic allelic expression

CpG island composition differences are a source of gene expression noise indicative of promoter responsiveness.

Deciphering the genetic architecture of variation in the immune response to Mycobacterium tuberculosis infection

Defining murine organogenesis at single-cell resolution reveals a role for the leukotriene pathway in regulating blood progenitor formation.

Detection and removal of barcode swapping in single-cell RNA-seq data

Differentiation dynamics of mammary epithelial cells revealed by single-cell RNA sequencing

Distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

ESR1 gene amplification in breast cancer: a common phenomenon?

Effect of read-mapping biases on detecting allele-specific expression from RNA-sequencing data

Effects of a brief course of azithromycin on soluble cell adhesion molecules and markers of inflammation in survivors of an acute coronary syndrome: A double-blind, randomized, placebo-controlled study

EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data

Expression Atlas update--a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments

Expression Atlas update: gene and protein expression in multiple species

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

Functional comparison of innate immune signaling pathways in primates

Gene expression differences among primates are associated with changes in a histone epigenetic modification

Genome-wide bisulfite sequencing in zygotes identifies demethylation targets and maps the contribution of TET3 oxidation.

Genomic-scale capture and sequencing of endogenous DNA from feces

Guidelines for reporting single-cell RNA-seq experiments

Heterogeneity in Oct4 and Sox2 Targets Biases Cell Fate in 4-Cell Mouse Embryos.

Hidden copy number variation in the HapMap population.

Hierarchical deconstruction of mouse olfactory sensory neurons: from whole mucosa to single-cell RNA-seq

High-resolution aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA-tRNA interface

High-throughput spatial mapping of single-cell RNA-seq data to tissue of origin

How Single-Cell Genomics Is Changing Evolutionary and Developmental Biology

IL-7-dependent compositional changes within the γδ T cell pool in lymph nodes during ageing lead to an unbalanced anti-tumour response

Identification of a regeneration-organizing cell in the Xenopus tail

Identifying cell types from spatially referenced single-cell expression datasets

Impact of Alternative Splicing on the Human Proteome

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data

Interplay of cis and trans mechanisms driving transcription factor binding and gene expression evolution.

Intratumor heterogeneity in human glioblastoma reflects cancer evolutionary dynamics.

Investigating higher-order interactions in single-cell data with scHOT

Isolation and Comparative Transcriptome Analysis of Human Fetal and iPSC-Derived Cone Photoreceptor Cells

LifeTime and improving European healthcare through cell-based interceptive medicine

Long-range enhancers regulating Myc expression are required for normal facial morphogenesis

Mapping Rora expression in resting and activated CD4+ T cells

Molecular and neuronal homology between the olfactory systems of zebrafish and mouse

Mosaic autosomal aneuploidies are detectable from single-cell RNAseq data

Multi-Omics Factor Analysis-a framework for unsupervised integration of multi-omics data sets.

Multi-species, multi-transcription factor binding highlights conserved control of tissue-specific biological pathways

Normalizing single-cell RNA sequencing data: challenges and opportunities

Numbers of copy-number variations and false-negative rates will be underestimated if we do not account for the dependence between repeated experiments

Overcoming confounding plate effects in differential expression analyses of single-cell RNA-seq data