Lista de obras -

A global view of pleiotropy and phenotypically derived gene function in yeast

artículo científico publicado en 2005

A global view of the selection forces in the evolution of yeast cis-regulation

artículo científico publicado en 2004

A probabilistic methodology for integrating knowledge and experiments on biological networks

artículo científico publicado en 2006

A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states

artículo científico publicado en 2020

A systematic approach to understand the functional consequences of non-protein coding risk regions

artículo científico publicado en 2010

Addiction of t(8;21) and inv(16) Acute Myeloid Leukemia to Native RUNX1 ⬇️

artículo científico publicado el 19 de septiembre de 2013

BLUEPRINT to decode the epigenetic signature written in blood

artículo científico publicado en 2012

Capturing pairwise and multi-way chromosomal conformations using chromosomal walks.

artículo científico publicado en 2016

Cell-Autonomous Function of Runx1 Transcriptionally Regulates Mouse Megakaryocytic Maturation ⬇️

artículo científico publicado el 23 de mayo de 2013

Cell-cycle dynamics of chromosomal organization at single-cell resolution.

artículo científico publicado en 2017

Chromosomal domains: epigenetic contexts and functional implications of genomic compartmentalization

artículo científico

Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

scientific article published on 31 May 2018

Cohesin-mediated interactions organize chromosomal domain architecture

artículo científico publicado en 2013

Combgap Promotes Ovarian Niche Development and Chromatin Association of EcR-Binding Regions in BR-C.

artículo científico publicado en 2016

Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture

artículo científico publicado en 2015

Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture.

artículo científico publicado en 2010

Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast

artículo científico publicado en 2005

Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting

artículo científico publicado en 2006

Cooperativity, specificity, and evolutionary stability of Polycomb targeting in Drosophila

artículo científico publicado en 2014

Corrigendum: Derivation of novel human ground state naive pluripotent stem cells

scientific article published on 01 April 2015

Corrigendum: Deterministic direct reprogramming of somatic cells to pluripotency

scientific article published on 01 April 2015

Corrigendum: p53 is essential for DNA methylation homeostasis in naïve embryonic stem cells, and its loss promotes clonal heterogeneity

artículo científico publicado en 2018

DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation

artículo científico publicado en 2021

DNA methylation programming and reprogramming in primate embryonic stem cells.

artículo científico publicado en 2009

Derivation of novel human ground state naive pluripotent stem cells

artículo científico publicado en 2013

Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

scientific article published on 13 December 2018

Deterministic direct reprogramming of somatic cells to pluripotency

artículo científico publicado en 2013

Discovering statistically significant biclusters in gene expression data

artículo científico publicado en 2002

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

artículo científico publicado en 2016

Dissecting cellular crosstalk by sequencing physically interacting cells

scientific article published on 09 March 2020

Donor cell leukemia: reappearance of gene mutations in donor cells - more than an incidental phenomenon?

scientific article published on 07 May 2020

Drosophila Functional Elements Are Embedded in Structurally Constrained Sequences ⬇️

artículo científico publicado el 30 de mayo de 2013

Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells

artículo científico publicado en 2014

Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models ⬇️

artículo científico publicado el 19 de octubre de 2010

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

scientific article published on 27 December 2018

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

scientific article published on 01 April 2020

EXPANDER--an integrative program suite for microarray data analysis

artículo científico publicado en 2005

Early metazoan cell type diversity and the evolution of multicellular gene regulation

article

Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues

artículo científico publicado en 2012

Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites

artículo científico publicado en 2008

Expander: from expression microarrays to networks and functions

artículo científico publicado en 2010

Extensive low-affinity transcriptional interactions in the yeast genome

artículo científico publicado en 2006

Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line

artículo científico publicado en 2008

Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos

artículo científico publicado en 2009

Functional enhancers at the gene-poor 8q24 cancer-linked locus.

artículo científico publicado en 2009

Global DNA methylation reflects spatial heterogeneity and molecular evolution of lung adenocarcinomas

article

H2A.Z Maintenance during Mitosis Reveals Nucleosome Shifting on Mitotically Silenced Genes ⬇️

artículo científico publicado el 24 de septiembre de 2010

Hyperconserved CpG domains underlie Polycomb-binding sites

artículo científico publicado en 2007

Hypomethylation marks enhancers within transposable elements

scientific article published on 01 July 2013

Inferring Divergence of Context-Dependent Substitution Rates in Drosophila Genomes with Applications to Comparative Genomics ⬇️

artículo científico publicado el 1 de febrero de 2012

Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium

artículo científico publicado en 2005

Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer.

artículo científico publicado en 2014

LifeTime and improving European healthcare through cell-based interceptive medicine

artículo científico publicado en 2020

MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing

artículo científico publicado en 2019

Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types

artículo científico publicado en 2014

MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions

scientific article published on 11 October 2019

Minreg: inferring an active regulator set.

artículo científico publicado en 2002

Modeling and analysis of heterogeneous regulation in biological networks

artículo científico publicado en 2004

Multilevel modeling and inference of transcription regulation

artículo científico publicado en 2004

Multiscale 3D Genome Rewiring during Mouse Neural Development

artículo científico publicado en 2017

Prediction of acute myeloid leukaemia risk in healthy individuals

scientific article published in Nature

Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection

artículo científico publicado en 2011

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

artículo científico publicado en 2011

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

artículo científico publicado en 2021

Quantification of protein half-lives in the budding yeast proteome

artículo científico publicado en 2006

Recurrent deletions in clonal hematopoiesis are driven by microhomology-mediated end joining

artículo científico publicado en 2021

Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data

artículo científico publicado en 2004

Robust 4C-seq data analysis to screen for regulatory DNA interactions.

artículo científico publicado en 2012

Scaling single-cell genomics from phenomenology to mechanism

artículo científico publicado en 2017

Sequence context affects the rate of short insertions and deletions in flies and primates

artículo científico publicado en 2008

Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma

artículo científico publicado en 2018

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell.

artículo científico publicado en 2015

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

artículo científico publicado en 2013

Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells

artículo científico publicado en 2020

Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis

artículo científico publicado en 2018

Single-cell epigenomics: techniques and emerging applications

artículo científico publicado en 2015

Suppressors and activators of JAK-STAT signaling at diagnosis and relapse of acute lymphoblastic leukemia in Down syndrome

artículo científico publicado en 2017

The EXPANDER Integrated Platform for Transcriptome Analysis

artículo científico publicado en 2019

The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome

artículo científico publicado en 2016

The mutation spectrum in genomic late replication domains shapes mammalian GC content

artículo científico publicado en 2016

Three-dimensional folding and functional organization principles of the Drosophila genome

artículo científico publicado en 2012

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

artículo científico publicado en 2015

Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors

artículo científico publicado en 2016

UMI-4C for quantitative and targeted chromosomal contact profiling.

artículo científico

Voices in methods development

artículo científico publicado en 2019

Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast

artículo científico publicado en 2010

p53 is essential for DNA methylation homeostasis in naïve embryonic stem cells, and its loss promotes clonal heterogeneity

artículo científico publicado en 2017

Lista de obras de

A global view of pleiotropy and phenotypically derived gene function in yeast

A global view of the selection forces in the evolution of yeast cis-regulation

A probabilistic methodology for integrating knowledge and experiments on biological networks

A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states

A systematic approach to understand the functional consequences of non-protein coding risk regions

Addiction of t(8;21) and inv(16) Acute Myeloid Leukemia to Native RUNX1 ⬇️

BLUEPRINT to decode the epigenetic signature written in blood

Capturing pairwise and multi-way chromosomal conformations using chromosomal walks.

Cell-Autonomous Function of Runx1 Transcriptionally Regulates Mouse Megakaryocytic Maturation ⬇️

Cell-cycle dynamics of chromosomal organization at single-cell resolution.

Chromosomal domains: epigenetic contexts and functional implications of genomic compartmentalization

Cnidarian Cell Type Diversity and Regulation Revealed by Whole-Organism Single-Cell RNA-Seq

Cohesin-mediated interactions organize chromosomal domain architecture

Combgap Promotes Ovarian Niche Development and Chromatin Association of EcR-Binding Regions in BR-C.

Comparative Hi-C reveals that CTCF underlies evolution of chromosomal domain architecture

Comparative analysis of DNA replication timing reveals conserved large-scale chromosomal architecture.

Conservation and evolvability in regulatory networks: the evolution of ribosomal regulation in yeast

Constitutive nucleosome depletion and ordered factor assembly at the GRP78 promoter revealed by single molecule footprinting

Cooperativity, specificity, and evolutionary stability of Polycomb targeting in Drosophila

Corrigendum: Derivation of novel human ground state naive pluripotent stem cells

Corrigendum: Deterministic direct reprogramming of somatic cells to pluripotency

Corrigendum: p53 is essential for DNA methylation homeostasis in naïve embryonic stem cells, and its loss promotes clonal heterogeneity

DNA methylation landscapes of 1538 breast cancers reveal a replication-linked clock, epigenomic instability and cis-regulation

DNA methylation programming and reprogramming in primate embryonic stem cells.

Derivation of novel human ground state naive pluripotent stem cells

Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules

Deterministic direct reprogramming of somatic cells to pluripotency

Discovering statistically significant biclusters in gene expression data

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

Dissecting cellular crosstalk by sequencing physically interacting cells

Donor cell leukemia: reappearance of gene mutations in donor cells - more than an incidental phenomenon?

Drosophila Functional Elements Are Embedded in Structurally Constrained Sequences ⬇️

Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells

Dynamic combinatorial interactions of RUNX1 and cooperating partners regulates megakaryocytic differentiation in cell line models ⬇️

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

Dysfunctional CD8 T Cells Form a Proliferative, Dynamically Regulated Compartment within Human Melanoma

EXPANDER--an integrative program suite for microarray data analysis

Early metazoan cell type diversity and the evolution of multicellular gene regulation

Epigenetic polymorphism and the stochastic formation of differentially methylated regions in normal and cancerous tissues

Evolution and selection in yeast promoters: analyzing the combined effect of diverse transcription factor binding sites

Expander: from expression microarrays to networks and functions

Extensive low-affinity transcriptional interactions in the yeast genome

Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line

Functional anatomy of polycomb and trithorax chromatin landscapes in Drosophila embryos

Functional enhancers at the gene-poor 8q24 cancer-linked locus.

Global DNA methylation reflects spatial heterogeneity and molecular evolution of lung adenocarcinomas

H2A.Z Maintenance during Mitosis Reveals Nucleosome Shifting on Mitotically Silenced Genes ⬇️

Hyperconserved CpG domains underlie Polycomb-binding sites

Hypomethylation marks enhancers within transposable elements

Inferring Divergence of Context-Dependent Substitution Rates in Drosophila Genomes with Applications to Comparative Genomics ⬇️

Integrative analysis of genome-wide experiments in the context of a large high-throughput data compendium

Intratumor DNA methylation heterogeneity reflects clonal evolution in aggressive prostate cancer.

LifeTime and improving European healthcare through cell-based interceptive medicine

MARS-seq2.0: an experimental and analytical pipeline for indexed sorting combined with single-cell RNA sequencing

Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types

MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions

Minreg: inferring an active regulator set.

Modeling and analysis of heterogeneous regulation in biological networks

Multilevel modeling and inference of transcription regulation

Multiscale 3D Genome Rewiring during Mouse Neural Development

Prediction of acute myeloid leukaemia risk in healthy individuals

Primate CpG islands are maintained by heterogeneous evolutionary regimes involving minimal selection

Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture

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

Quantification of protein half-lives in the budding yeast proteome

Recurrent deletions in clonal hematopoiesis are driven by microhomology-mediated end joining

Revealing modularity and organization in the yeast molecular network by integrated analysis of highly heterogeneous genomewide data

Robust 4C-seq data analysis to screen for regulatory DNA interactions.

Scaling single-cell genomics from phenomenology to mechanism

Sequence context affects the rate of short insertions and deletions in flies and primates

Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma

Single-cell Hi-C for genome-wide detection of chromatin interactions that occur simultaneously in a single cell.

Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

Single-cell analysis of clonal maintenance of transcriptional and epigenetic states in cancer cells

Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis

Single-cell epigenomics: techniques and emerging applications

Suppressors and activators of JAK-STAT signaling at diagnosis and relapse of acute lymphoblastic leukemia in Down syndrome

The EXPANDER Integrated Platform for Transcriptome Analysis

The Spectrum and Regulatory Landscape of Intestinal Innate Lymphoid Cells Are Shaped by the Microbiome