Lista de obras - Shyam Prabhakar - Dominio Público Uruguay

A developmental transcriptomic analysis of Pax1 and Pax9 in embryonic intervertebral disc development.

artículo científico publicado en 2017

A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus

artículo científico publicado en 2017

A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data

artículo científico publicado en 2016

ACSL1 Is Associated With Fetal Programming of Insulin Sensitivity and Cellular Lipid Content

artículo científico publicado en 2015

Accelerated evolution of conserved noncoding sequences in humans

artículo científico publicado en 2006

An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos

artículo científico publicado en 2017

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences

artículo científico publicado en 2005

Author Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

artículo científico publicado en 2018

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

artículo científico publicado en 2006

Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters

artículo científico publicado en 2016

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

artículo científico publicado en 2013

Concurrent Single-Cell RNA and Targeted DNA Sequencing on an Automated Platform for Comeasurement of Genomic and Transcriptomic Signatures

scientific article published on 06 December 2018

DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1.

artículo científico publicado en 2018

DUBStepR: correlation-based feature selection for clustering single-cell RNA sequencing data ⬇️

artículo científico publicado en 2020

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements ⬇️

artículo científico publicado el 16 de febrero de 2012

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons

artículo científico publicado en 2007

Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development

scientific article published on 01 April 2020

Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations.

artículo científico publicado en 2014

Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype

scientific article published on 12 June 2020

Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A.

artículo científico publicado en 2005

Gene expression profiles of Bapx1 expressing FACS sorted cells from wildtype and Bapx1-EGFP null mouse embryos

artículo científico publicado en 2015

Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish

artículo científico publicado en 2013

Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro

artículo científico publicado en 2016

Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue

artículo científico publicado en 2019

Histone Acetylome-wide Association Study of Autism Spectrum Disorder.

artículo científico publicado en 2016

Human-specific gain of function in a developmental enhancer

artículo científico publicado en 2008

In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures

artículo científico publicado en 2013

In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column

artículo científico publicado en 2014

Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism

scientific article published on 25 September 2020

Integrative model of genomic factors for determining binding site selection by estrogen receptor-α

artículo científico publicado en 2010

Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease

scientific article published on 23 April 2019

Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer

artículo científico publicado en 2020

MLL fusion proteins preferentially regulate a subset of wild-type MLL target genes in the leukemic genome ⬇️

artículo científico publicado el 25 de abril de 2011

Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny

artículo científico publicado en 2005

Massive contribution of transposable elements to mammalian regulatory sequences

artículo científico publicado en 2016

Meta-analysis identifies novel risk loci and yields systematic insights into the biology of male-pattern baldness

artículo científico publicado en 2017

MiR-135b is a direct PAX6 target and specifies human neuroectoderm by inhibiting TGF-β/BMP signaling

artículo científico publicado en 2014

Ncoa3 functions as an essential Esrrb coactivator to sustain embryonic stem cell self-renewal and reprogramming

scientific journal article

Non-canonical NF-κB signalling and ETS1/2 cooperatively drive C250T mutant TERT promoter activation.

artículo científico publicado en 2015

Noncoding origins of anthropoid traits and a new null model of transposon functionalization

artículo científico publicado en 2014

Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-Wild-Type Diffuse Astrocytic Gliomas

scientific article published on 20 August 2019

Primate-specific evolution of an LDLR enhancer

artículo científico publicado en 2006

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

artículo científico publicado en 2017

Resistin expression in human monocytes is controlled by two linked promoter SNPs mediating NFKB p50/p50 binding and C-methylation

artículo científico publicado en 2019

Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress-Gene Response

artículo científico publicado en 2019

Robust clustering and interpretation of scRNA-seq data using reference component analysis

artículo científico publicado en 2021

Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data

artículo científico publicado en 2016

Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer

artículo científico publicado en 2007

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains

artículo científico publicado en 2015

Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms

artículo científico publicado en 2015

Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF- effectors

artículo científico publicado en 2010

Study sequence rules of estrogen receptor α–DNA interactions using dual polarization interferometry and computational modeling ⬇️

artículo científico publicado el 23 de octubre de 2012

TACO: a general-purpose tool for predicting cell-type-specific transcription factor dimers.

artículo científico publicado en 2014

The DNA sequence and comparative analysis of human chromosome 5

artículo científico publicado en 2004

The PsychENCODE project

artículo científico publicado en 2015

The sequence and analysis of duplication-rich human chromosome 16

artículo científico publicado en 2004

The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis

artículo científico publicado en 2016

TherMos: Estimating protein-DNA binding energies from in vivo binding profiles

artículo científico publicado en 2013

Tumor-derived circulating endothelial cell clusters in colorectal cancer

artículo científico publicado en 2016

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

artículo científico publicado en 2008

Uniform, optimal signal processing of mapped deep-sequencing data

artículo científico publicado en 2013

scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data ⬇️

artículo científico publicado en 2020

Lista de obras de Shyam Prabhakar

A developmental transcriptomic analysis of Pax1 and Pax9 in embryonic intervertebral disc development.

A functional SNP associated with atopic dermatitis controls cell type-specific methylation of the VSTM1 gene locus

A machine learning approach for the identification of key markers involved in brain development from single-cell transcriptomic data

ACSL1 Is Associated With Fetal Programming of Insulin Sensitivity and Cellular Lipid Content

Accelerated evolution of conserved noncoding sequences in humans

An Integrative Developmental Genomics and Systems Biology Approach to Identify an In Vivo Sox Trio-Mediated Gene Regulatory Network in Murine Embryos

Annotation of cis-regulatory elements by identification, subclassification, and functional assessment of multispecies conserved sequences

Author Correction: Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

Close sequence comparisons are sufficient to identify human cis-regulatory elements.

Comprehensive benchmarking reveals H2BK20 acetylation as a distinctive signature of cell-state-specific enhancers and promoters

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

Concurrent Single-Cell RNA and Targeted DNA Sequencing on an Automated Platform for Comeasurement of Genomic and Transcriptomic Signatures

DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1.

DUBStepR: correlation-based feature selection for clustering single-cell RNA sequencing data ⬇️

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements ⬇️

Detection of weakly conserved ancestral mammalian regulatory sequences by primate comparisons

Early Fate Defines Microglia and Non-parenchymal Brain Macrophage Development

Efficient endoderm induction from human pluripotent stem cells by logically directing signals controlling lineage bifurcations.

Epigenomes of Human Hearts Reveal New Genetic Variants Relevant for Cardiac Disease and Phenotype

Gene expression patterns define key transcriptional events in cell-cycle regulation by cAMP and protein kinase A.

Gene expression profiles of Bapx1 expressing FACS sorted cells from wildtype and Bapx1-EGFP null mouse embryos

Genome wide analysis reveals Zic3 interaction with distal regulatory elements of stage specific developmental genes in zebrafish

Genome wide binding (ChIP-Seq) of murine Bapx1 and Sox9 proteins in vivo and in vitro

Genome-wide DNA methylation profiling identifies convergent molecular signatures associated with idiopathic and syndromic autism in post-mortem human brain tissue

Histone Acetylome-wide Association Study of Autism Spectrum Disorder.

Human-specific gain of function in a developmental enhancer

In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures

In vivo genome-wide analysis of multiple tissues identifies gene regulatory networks, novel functions and downstream regulatory genes for Bapx1 and its co-regulation with Sox9 in the mammalian vertebral column

Integrative genomics identifies a convergent molecular subtype that links epigenomic with transcriptomic differences in autism

Integrative model of genomic factors for determining binding site selection by estrogen receptor-α

Intrinsic mutant HTT-mediated defects in oligodendroglia cause myelination deficits and behavioral abnormalities in Huntington disease

Lineage-dependent gene expression programs influence the immune landscape of colorectal cancer

MLL fusion proteins preferentially regulate a subset of wild-type MLL target genes in the leukemic genome ⬇️

Mapping cis-regulatory domains in the human genome using multi-species conservation of synteny

Massive contribution of transposable elements to mammalian regulatory sequences

Meta-analysis identifies novel risk loci and yields systematic insights into the biology of male-pattern baldness

MiR-135b is a direct PAX6 target and specifies human neuroectoderm by inhibiting TGF-β/BMP signaling

Ncoa3 functions as an essential Esrrb coactivator to sustain embryonic stem cell self-renewal and reprogramming

Non-canonical NF-κB signalling and ETS1/2 cooperatively drive C250T mutant TERT promoter activation.

Noncoding origins of anthropoid traits and a new null model of transposon functionalization

Pathogenic Epigenetic Consequences of Genetic Alterations in IDH-Wild-Type Diffuse Astrocytic Gliomas

Primate-specific evolution of an LDLR enhancer

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

Resistin expression in human monocytes is controlled by two linked promoter SNPs mediating NFKB p50/p50 binding and C-methylation

Robust CTCF-Based Chromatin Architecture Underpins Epigenetic Changes in the Heart Failure Stress-Gene Response

Robust clustering and interpretation of scRNA-seq data using reference component analysis

Romulus: robust multi-state identification of transcription factor binding sites from DNase-seq data

Runx1-mediated hematopoietic stem-cell emergence is controlled by a Gata/Ets/SCL-regulated enhancer

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains

Sensitive detection of chromatin-altering polymorphisms reveals autoimmune disease mechanisms

Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF- effectors

Study sequence rules of estrogen receptor α–DNA interactions using dual polarization interferometry and computational modeling ⬇️

TACO: a general-purpose tool for predicting cell-type-specific transcription factor dimers.

The DNA sequence and comparative analysis of human chromosome 5

The PsychENCODE project

The sequence and analysis of duplication-rich human chromosome 16

The transcription factor SOX6 contributes to the developmental origins of obesity by promoting adipogenesis

TherMos: Estimating protein-DNA binding energies from in vivo binding profiles

Tumor-derived circulating endothelial cell clusters in colorectal cancer

Ultraconservation identifies a small subset of extremely constrained developmental enhancers

Uniform, optimal signal processing of mapped deep-sequencing data

scConsensus: combining supervised and unsupervised clustering for cell type identification in single-cell RNA sequencing data ⬇️