Lista de obras -

A dominated coupling from the past algorithm for the stochastic simulation of networks of biochemical reactions

artículo científico publicado en 2008

A robust activity marking system for exploring active neuronal ensembles.

artículo científico publicado en 2016

Adult Human Glioblastomas Harbor Radial Glia-like Cells

scientific article published on 30 January 2020

Adult Human Glioblastomas Harbor Radial Glia-like Cells

scientific article published on 01 July 2020

Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

artículo científico publicado en 2020

Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences

artículo científico publicado en 2020

Bhlhb5 and Prdm8 Form a Repressor Complex Involved in Neuronal Circuit Assembly ⬇️

artículo científico publicado el 26 de enero de 2012

Challenges in unsupervised clustering of single-cell RNA-seq data

artículo científico publicado en 2019

Chromatin remodeling inactivates activity genes and regulates neural coding

artículo científico publicado en 2016

Computational Stem Cell Biology: Open Questions and Guiding Principles

artículo científico publicado en 2021

Conservation of transcription factor binding events predicts gene expression across species ⬇️

artículo científico publicado el 26 de mayo de 2011

Discrete distributional differential expression (D3E)--a tool for gene expression analysis of single-cell RNA-seq data

artículo científico publicado en 2016

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

artículo científico publicado en 2015

Enhancer RNAs: a class of long noncoding RNAs synthesized at enhancers

artículo científico

False signals induced by single-cell imputation

scientific article published on 02 November 2018

Fast searches of large collections of single-cell data using scfind

artículo científico publicado en 2021

Genome-Wide Activity-Dependent MeCP2 Phosphorylation Regulates Nervous System Development and Function ⬇️

artículo científico publicado el 6 de octubre de 2011

Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection

artículo científico publicado en 2008

Genome-wide identification and characterization of functional neuronal activity-dependent enhancers

artículo científico publicado en 2014

Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways

artículo científico publicado en 2010

Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci

Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci.

artículo científico publicado en 2018

High-throughput functional comparison of promoter and enhancer activities

artículo científico publicado en 2016

Identifying cell populations with scRNASeq.

artículo científico

Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites

artículo científico publicado en 2012

M3Drop: dropout-based feature selection for scRNASeq

scientific article published on 01 August 2019

MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers

artículo científico publicado en 2015

MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments

artículo científico publicado en 2016

MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development

artículo científico publicado en 2020

Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis.

artículo científico publicado en 2018

Obstacles to detecting isoforms using full-length scRNA-seq data

scientific article published on 23 March 2020

Perfect sampling of the master equation for gene regulatory networks

artículo científico publicado en 2007

Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment

artículo científico publicado en 2017

Promoter decommissioning by the NuRD chromatin remodeling complex triggers synaptic connectivity in the mammalian brain

scientific journal article

Publisher Correction: Challenges in unsupervised clustering of single-cell RNA-seq data

scientific article published on 01 May 2019

Quantification of mRNA in single cells and modelling of RT-qPCR induced noise

artículo científico publicado en 2008

Quantitative profiling of peptides from RNAs classified as noncoding

artículo científico publicado en 2014

Quantitative transcription factor analysis of undifferentiated single human embryonic stem cells

artículo científico publicado en 2009

SC3: consensus clustering of single-cell RNA-seq data

artículo científico publicado en 2017

Simulation-based benchmarking of isoform quantification in single-cell RNA-seq

scientific article published on 07 November 2018

Single-cell genomics

scientific article published on 01 July 2018

Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis

artículo científico publicado en 2018

Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes

artículo científico publicado en 2020

Stochastic kinetics of viral capsid assembly based on detailed protein structures.

artículo científico publicado en 2006

Summing up the parts of the hypothalamus

artículo científico publicado en 2017

Supervised clustering for single-cell analysis

artículo científico publicado en 2019

Tau promotes neurodegeneration through global chromatin relaxation

artículo científico publicado en 2014

Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution

artículo científico publicado en 2017

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription. ⬇️

artículo científico publicado en 2017

The Human Cell Atlas

artículo científico publicado en 2017

The Human Cell Atlas

The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle

artículo científico publicado en 2019

The Malaria Cell Atlas: a comprehensive reference of single parasite transcriptomes across the complete Plasmodium life cycle: file S1

artículo científico publicado en 2019

Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts

artículo científico publicado en 2020

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

artículo científico publicado en 2008

TransposonUltimate: software for transposon classification, annotation and detection

artículo científico publicado en 2022

TransposonUltimate: software for transposon classification, annotation and detection

artículo científico publicado en 2021

Trophic levels and trophic tangles: the prevalence of omnivory in real food webs

artículo científico publicado en 2007

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

scientific article published on 07 December 2020

f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome

artículo científico publicado en 2016

scmap: projection of single-cell RNA-seq data across data sets

artículo científico publicado en 2018

Lista de obras de

A dominated coupling from the past algorithm for the stochastic simulation of networks of biochemical reactions

A robust activity marking system for exploring active neuronal ensembles.

Adult Human Glioblastomas Harbor Radial Glia-like Cells

Adult Human Glioblastomas Harbor Radial Glia-like Cells

Astrocyte layers in the mammalian cerebral cortex revealed by a single-cell in situ transcriptomic map

Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences

Bhlhb5 and Prdm8 Form a Repressor Complex Involved in Neuronal Circuit Assembly ⬇️

Challenges in unsupervised clustering of single-cell RNA-seq data

Chromatin remodeling inactivates activity genes and regulates neural coding

Computational Stem Cell Biology: Open Questions and Guiding Principles

Conservation of transcription factor binding events predicts gene expression across species ⬇️

Discrete distributional differential expression (D3E)--a tool for gene expression analysis of single-cell RNA-seq data

Disruption of DNA-methylation-dependent long gene repression in Rett syndrome

Enhancer RNAs: a class of long noncoding RNAs synthesized at enhancers

False signals induced by single-cell imputation

Fast searches of large collections of single-cell data using scfind

Genome-Wide Activity-Dependent MeCP2 Phosphorylation Regulates Nervous System Development and Function ⬇️

Genome-wide analysis of MEF2 transcriptional program reveals synaptic target genes and neuronal activity-dependent polyadenylation site selection

Genome-wide identification and characterization of functional neuronal activity-dependent enhancers

Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways

Genomic positional conservation identifies topological anchor point (tap)RNAs linked to developmental loci

Genomic positional conservation identifies topological anchor point RNAs linked to developmental loci.

High-throughput functional comparison of promoter and enhancer activities

Identifying cell populations with scRNASeq.

Integrated genome analysis suggests that most conserved non-coding sequences are regulatory factor binding sites

M3Drop: dropout-based feature selection for scRNASeq

MEF2D drives photoreceptor development through a genome-wide competition for tissue-specific enhancers

MPRAnator: a web-based tool for the design of massively parallel reporter assay experiments

MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development

Noncanonical secondary structures arising from non-B DNA motifs are determinants of mutagenesis.

Obstacles to detecting isoforms using full-length scRNA-seq data

Perfect sampling of the master equation for gene regulatory networks

Proliferation Drives Aging-Related Functional Decline in a Subpopulation of the Hematopoietic Stem Cell Compartment

Promoter decommissioning by the NuRD chromatin remodeling complex triggers synaptic connectivity in the mammalian brain

Publisher Correction: Challenges in unsupervised clustering of single-cell RNA-seq data

Quantification of mRNA in single cells and modelling of RT-qPCR induced noise

Quantitative profiling of peptides from RNAs classified as noncoding

Quantitative transcription factor analysis of undifferentiated single human embryonic stem cells

SC3: consensus clustering of single-cell RNA-seq data

Simulation-based benchmarking of isoform quantification in single-cell RNA-seq

Single-cell genomics

Single-cell transcriptomics reveals a new dynamical function of transcription factors during embryonic hematopoiesis

Souporcell: robust clustering of single-cell RNA-seq data by genotype without reference genotypes

Stochastic kinetics of viral capsid assembly based on detailed protein structures.

Summing up the parts of the hypothalamus

Supervised clustering for single-cell analysis

Tau promotes neurodegeneration through global chromatin relaxation

Temporal Tracking of Microglia Activation in Neurodegeneration at Single-Cell Resolution

The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription. ⬇️

The Human Cell Atlas

The Human Cell Atlas

The Malaria Cell Atlas: Single parasite transcriptomes across the complete Plasmodium life cycle

The Malaria Cell Atlas: a comprehensive reference of single parasite transcriptomes across the complete Plasmodium life cycle: file S1

Transcription-coupled repair and mismatch repair contribute towards preserving genome integrity at mononucleotide repeat tracts

Transcriptome-wide noise controls lineage choice in mammalian progenitor cells

TransposonUltimate: software for transposon classification, annotation and detection

TransposonUltimate: software for transposon classification, annotation and detection

Trophic levels and trophic tangles: the prevalence of omnivory in real food webs

Tutorial: guidelines for the computational analysis of single-cell RNA sequencing data

f-divergence cutoff index to simultaneously identify differential expression in the integrated transcriptome and proteome

scmap: projection of single-cell RNA-seq data across data sets