Lista de obras - Nir Friedman - Dominio Público Uruguay

A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families

artículo científico publicado en 2002

A functional and regulatory map of asthma

artículo científico publicado en 2007

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks

artículo científico publicado en 2012

A gamma mixture model better accounts for among site rate heterogeneity

artículo científico publicado en 2005

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals

artículo científico publicado en 2012

A module map showing conditional activity of expression modules in cancer

artículo científico publicado en 2004

A novel Bayesian DNA motif comparison method for clustering and retrieval

artículo científico publicado en 2008

A structural EM algorithm for phylogenetic inference

artículo científico publicado en 2002

A synthetic biology approach to probing nucleosome symmetry.

artículo científico publicado en 2017

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

artículo científico publicado en 2009

Ab initio prediction of transcription factor targets using structural knowledge

artículo científico publicado en 2005

An integrative clustering and modeling algorithm for dynamical gene expression data ⬇️

artículo científico publicado en 2011

Author Correction: Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

artículo científico publicado en 2020

Automatic genome-wide reconstruction of phylogenetic gene trees

artículo científico publicado en 2007

Bayesian Network Classifiers

Being Bayesian About Network Structure. A Bayesian Approach to Structure Discovery in Bayesian Networks

Blood transcriptional signatures of multiple sclerosis: unique gene expression of disease activity

artículo científico publicado en 2004

CIS: compound importance sampling method for protein-DNA binding site p-value estimation

artículo científico publicado en 2004

Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast

artículo científico publicado en 2008

Charting a tissue from single-cell transcriptomes

Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis

artículo científico publicado en 2015

Clk post-transcriptional control denoises circadian transcription both temporally and spatially

artículo científico publicado en 2015

Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays

artículo científico publicado en 2004

Comparative functional genomics of the fission yeasts

artículo científico publicado en 2011

Comprehensive Mapping of DNA Damage: From Static Genetic Maps to Condition-Specific Maps

Condition-specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response

artículo científico publicado en 2015

Context-specific Bayesian clustering for gene expression data

artículo científico publicado en 2002

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

artículo científico publicado en 2013

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

scientific article published on 02 December 2019

Densely interconnected transcriptional circuits control cell states in human hematopoiesis

artículo científico publicado en 2011

Dynamics of Replication-Independent Histone Turnover in Budding Yeast

artículo científico publicado en 2007

Dynamics of Sir3 spreading in budding yeast: secondary recruitment sites and euchromatic localization

artículo científico publicado en 2011

Efficient Exact p -Value Computation for Small Sample, Sparse, and Surprising Categorical Data

scholarly article by Gill Bejerano published in October 2004

Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution.

artículo científico publicado en 2016

Elucidating Combinatorial Chromatin States by Co-ImmunoPrecipitation (comb-ChIP)

Epigenomics and the structure of the living genome

artículo científico publicado en 2015

Erratum: Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivors

article

Exploring transcription regulation through cell-to-cell variability

artículo científico publicado en 2011

From large-scale assays to mechanistic insights: computational analysis of interactions

artículo científico publicado en 2010

From signatures to models: understanding cancer using microarrays

artículo científico publicado en 2005

Full-length transcriptome assembly from RNA-Seq data without a reference genome

artículo científico publicado en 2011

Genetic screen of the yeast environmental stress response dynamics uncovers distinct regulatory phases

scientific article published on 01 August 2019

Genetics. The DNA damage road map.

artículo científico publicado en 2010

High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells

artículo científico publicado en 2011

High-resolution chromatin dynamics during a yeast stress response

artículo científico publicado en 2015

High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies

artículo científico publicado en 2014

High-resolution view of the yeast meiotic program revealed by ribosome profiling

artículo científico publicado en 2012

Human and porcine early kidney precursors as a new source for transplantation

Identifying novel constrained elements by exploiting biased substitution patterns

artículo científico publicado en 2009

Immunogenetics. Chromatin state dynamics during blood formation

artículo científico publicado en 2014

Inferring cellular networks using probabilistic graphical models

artículo científico publicado en 2004

Inferring quantitative models of regulatory networks from expression data

artículo científico publicado en 2004

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

artículo científico publicado en 2015

Mapping the Landscape of a Eukaryotic Degronome.

artículo científico publicado en 2016

Mitochondrial processes are impaired in hereditary inclusion body myopathy.

artículo científico publicado en 2008

Modeling belief in dynamic systems, part I: Foundations

Modularity and directionality in genetic interaction maps

artículo científico publicado en 2010

Multivariate information bottleneck

artículo científico publicado en 2006

Natural history and evolutionary principles of gene duplication in fungi

artículo científico publicado en 2007

Nucleosome positioning from tiling microarray data

artículo científico publicado en 2008

On decision-theoretic foundations for defaults

Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals

artículo científico publicado en 2010

Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivors

artículo científico publicado en 2005

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

artículo científico publicado en 2016

Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates

artículo científico publicado en 2007

Plausibility measures and default reasoning

RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast

artículo científico publicado en 2010

Replication and active demethylation represent partially overlapping mechanisms for erasure of H3K4me3 in budding yeast

artículo científico publicado en 2010

S.16.04 Peripheral gene expression in PTSD

article

Selective flexible packaging pathways of the segmented genome of influenza A virus

artículo científico publicado en 2020

Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression

artículo científico publicado en 2004

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

artículo científico publicado en 2014

Single-nucleosome mapping of histone modifications in S. cerevisiae

artículo científico publicado en 2005

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

artículo científico publicado en 2010

Stress-related genomic responses during the course of heat acclimation and its association with ischemic-reperfusion cross-tolerance.

artículo científico publicado en 2004

Structure and function of a transcriptional network activated by the MAPK Hog1.

artículo científico publicado en 2008

Systematic dissection of roles for chromatin regulators in a yeast stress response

artículo científico publicado en 2012

Temporal profiling of redox-dependent heterogeneity in single cells

Temporal profiling of redox-dependent heterogeneity in single cells.

artículo científico publicado en 2018

Tissue classification with gene expression profiles.

artículo científico publicado en 2000

Towards an integrated protein-protein interaction network: a relational Markov network approach

artículo científico publicado en 2006

Transcriptional Profiling of Non-small Cell Lung Cancer Using Oligonucleotide Microarrays

artículo científico publicado en 2002

Using Bayesian networks to analyze expression data

artículo científico publicado en 2000

Lista de obras de Nir Friedman

A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families

A functional and regulatory map of asthma

A functional selection model explains evolutionary robustness despite plasticity in regulatory networks

A gamma mixture model better accounts for among site rate heterogeneity

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals

A module map showing conditional activity of expression modules in cancer

A novel Bayesian DNA motif comparison method for clustering and retrieval

A structural EM algorithm for phylogenetic inference

A synthetic biology approach to probing nucleosome symmetry.

Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing

Ab initio prediction of transcription factor targets using structural knowledge

An integrative clustering and modeling algorithm for dynamical gene expression data ⬇️

Author Correction: Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

Automatic genome-wide reconstruction of phylogenetic gene trees

Bayesian Network Classifiers

Being Bayesian About Network Structure. A Bayesian Approach to Structure Discovery in Bayesian Networks

Blood transcriptional signatures of multiple sclerosis: unique gene expression of disease activity

CIS: compound importance sampling method for protein-DNA binding site p-value estimation

Cell cycle- and chaperone-mediated regulation of H3K56ac incorporation in yeast

Charting a tissue from single-cell transcriptomes

Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis

Clk post-transcriptional control denoises circadian transcription both temporally and spatially

Comparative analysis of algorithms for signal quantitation from oligonucleotide microarrays

Comparative functional genomics of the fission yeasts

Comprehensive Mapping of DNA Damage: From Static Genetic Maps to Condition-Specific Maps

Condition-specific genetic interaction maps reveal crosstalk between the cAMP/PKA and the HOG MAPK pathways in the activation of the general stress response

Context-specific Bayesian clustering for gene expression data

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters

Densely interconnected transcriptional circuits control cell states in human hematopoiesis

Dynamics of Replication-Independent Histone Turnover in Budding Yeast

Dynamics of Sir3 spreading in budding yeast: secondary recruitment sites and euchromatic localization

Efficient Exact p -Value Computation for Small Sample, Sparse, and Surprising Categorical Data

Elucidating Combinatorial Chromatin States at Single-Nucleosome Resolution.

Elucidating Combinatorial Chromatin States by Co-ImmunoPrecipitation (comb-ChIP)

Epigenomics and the structure of the living genome

Erratum: Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivors

Exploring transcription regulation through cell-to-cell variability

From large-scale assays to mechanistic insights: computational analysis of interactions

From signatures to models: understanding cancer using microarrays

Full-length transcriptome assembly from RNA-Seq data without a reference genome

Genetic screen of the yeast environmental stress response dynamics uncovers distinct regulatory phases

Genetics. The DNA damage road map.

High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells

High-resolution chromatin dynamics during a yeast stress response

High-resolution sequencing and modeling identifies distinct dynamic RNA regulatory strategies

High-resolution view of the yeast meiotic program revealed by ribosome profiling

Human and porcine early kidney precursors as a new source for transplantation

Identifying novel constrained elements by exploiting biased substitution patterns

Immunogenetics. Chromatin state dynamics during blood formation

Inferring cellular networks using probabilistic graphical models

Inferring quantitative models of regulatory networks from expression data

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C

Mapping the Landscape of a Eukaryotic Degronome.

Mitochondrial processes are impaired in hereditary inclusion body myopathy.

Modeling belief in dynamic systems, part I: Foundations

Modularity and directionality in genetic interaction maps

Multivariate information bottleneck

Natural history and evolutionary principles of gene duplication in fungi

Nucleosome positioning from tiling microarray data

On decision-theoretic foundations for defaults

Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals

Peripheral blood mononuclear cell gene expression profiles identify emergent post-traumatic stress disorder among trauma survivors

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

Phylogeny reconstruction: increasing the accuracy of pairwise distance estimation using Bayesian inference of evolutionary rates

Plausibility measures and default reasoning

RNA polymerase mapping during stress responses reveals widespread nonproductive transcription in yeast

Replication and active demethylation represent partially overlapping mechanisms for erasure of H3K4me3 in budding yeast

S.16.04 Peripheral gene expression in PTSD

Selective flexible packaging pathways of the segmented genome of influenza A virus

Sfp1 is a stress- and nutrient-sensitive regulator of ribosomal protein gene expression

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

Single-nucleosome mapping of histone modifications in S. cerevisiae

Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species

Stress-related genomic responses during the course of heat acclimation and its association with ischemic-reperfusion cross-tolerance.

Structure and function of a transcriptional network activated by the MAPK Hog1.

Systematic dissection of roles for chromatin regulators in a yeast stress response

Temporal profiling of redox-dependent heterogeneity in single cells

Temporal profiling of redox-dependent heterogeneity in single cells.